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Bedair A, Hamed M, Mansour FR. Reshaping Capillary Electrophoresis With State-of-the-Art Sample Preparation Materials: Exploring New Horizons. Electrophoresis 2024. [PMID: 39345230 DOI: 10.1002/elps.202400114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/12/2024] [Accepted: 09/02/2024] [Indexed: 10/01/2024]
Abstract
Capillary electrophoresis (CE) is a powerful analysis technique with advantages such as high separation efficiency with resolution factors above 1.5, low sample consumption of less than 10 µL, cost-effectiveness, and eco-friendliness such as reduced solvent use and lower operational costs. However, CE also faces limitations, including limited detection sensitivity for low-concentration samples and interference from complex biological matrices. Prior to performing CE, it is common to utilize sample preparation procedures such as solid-phase microextraction (SPME) and liquid-phase microextraction (LPME) in order to improve the sensitivity and selectivity of the analysis. Recently, there have been advancements in the development of novel materials that have the potential to greatly enhance the performance of SPME and LPME. This review examines various materials and their uses in microextraction when combined with CE. These materials include carbon nanotubes, covalent organic frameworks, metal-organic frameworks, graphene and its derivatives, molecularly imprinted polymers, layered double hydroxides, ionic liquids, and deep eutectic solvents. The utilization of these innovative materials in extraction methods is being examined. Analyte recoveries and detection limits attained for a range of sample matrices are used to assess their effects on extraction selectivity, sensitivity, and efficiency. Exploring new materials for use in sample preparation techniques is important as it enables researchers to address current limitations of CE. The development of novel materials has the potential to greatly enhance extraction selectivity, sensitivity, and efficiency, thereby improving CE performance for complex biological analysis.
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Affiliation(s)
- Alaa Bedair
- Department of Analytical Chemistry, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt
| | - Mahmoud Hamed
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Cairo, Egypt
| | - Fotouh R Mansour
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Tanta University, Tanta, Egypt
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2
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Chen W, Zhang K, Huang F, Zhao L, Waldren GC, Jiang Q, Chen SX, Wang B, Guo W, Zhang DY, Zhang JX. Advancing quantitative PCR with color cycle multiplex amplification. Nucleic Acids Res 2024; 52:e81. [PMID: 39119904 PMCID: PMC11417387 DOI: 10.1093/nar/gkae683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/01/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024] Open
Abstract
Quantitative PCR (qPCR) is the gold standard for detection and quantitation of known DNA targets, but the scarcity of spectrally distinct fluorophores and filter sets limits the number of detectable targets. Here, we introduce color cycle multiplex amplification (CCMA) to significantly increase the number of detectable DNA targets in a single qPCR reaction using standard instrumentation. In CCMA, presence of one DNA target species results in a pre-programmed pattern of fluorescence increases. This pattern is distinguished by cycle thresholds (Cts) through rationally designed delays in amplification. For example, we design an assay wherein Staphylococcus aureus sequentially induces FAM, then Cy5.5, then ROX fluorescence increases with more than 3 cycles between each signal. CCMA offers notably higher potential for multiplexing because it uses fluorescence permutation rather than combination. With 4 distinct fluorescence colors, CCMA theoretically allows the detection of up to 136 distinct DNA target sequences using fluorescence permutation. Experimentally, we demonstrated a single-tube qPCR assay screening 21 sepsis-related bacterial DNA targets in samples of blood, sputum, pleural effusion and bronchoalveolar lavage fluid, with 89% clinical sensitivity and 100% clinical specificity, showing its potential as a powerful tool for advanced quantitative screening in molecular diagnostics.
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Affiliation(s)
- Wei Chen
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
| | - Kerou Zhang
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
| | - Fei Huang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, Shanghai 200032, China
| | - Lan Zhao
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | | | - Qi Jiang
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
| | - Sherry X Chen
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
| | - Bonnie Wang
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
| | - Wei Guo
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, Shanghai 200032, China
| | - David Y Zhang
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
| | - Jinny X Zhang
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
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Hoffmann A, Timm A, Johnson C, Rupp S, Grumaz C. Automation of customizable library preparation for next-generation sequencing into an open microfluidic platform. Sci Rep 2024; 14:17150. [PMID: 39060329 PMCID: PMC11282295 DOI: 10.1038/s41598-024-67950-6] [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: 12/12/2023] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Next-generation sequencing (NGS) is becoming more relevant for medical diagnostics, especially for using cell-free DNA to monitor response to therapy in cancer management, as high sensitivity of NGS enables detection of rare events. Sequencing Library preparation is a time-consuming and complex process, and large-scale liquid handlers are often used for automation. However, for smaller labs and low-to-medium throughput samples, these liquid handlers are expensive and need experts for handling. This work presents a proof-of-concept for library preparation on a commercially available and open lab-on-a-chip platform, which provides an alternative automation for low-to-medium throughput requirements. It covers common library preparation steps optimized to a microfluidic environment that include customizable PCR for target enrichment, end-repair, adapter ligation, nucleic acid purification via magnetic beads, and an integrated quantification step. The functionality of the cartridge is demonstrated with reference cfDNA containing different allelic frequencies of seven known mutations. Processing the samples in the cartridge reveals highly comparable results to manual processing (Pearson r = 0.94) based on amplicon sequencing. Summarized, the proposed automated lab-on-a-chip workflow for customizable library preparation could further pave the way for NGS to evolve from a technology used for research purposes to one that is applied in routine cancer management.
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Affiliation(s)
- Anne Hoffmann
- Institute of Interfacial Process Engineering and Plasma Technology, University of Stuttgart, Nobelstraße 12, 70569, Stuttgart, Germany
- Corporate Sector Research and Advance Engineering, Robert Bosch GmbH, Robert-Bosch-Campus 1, 71272, Renningen, Germany
| | - Anke Timm
- Corporate Sector Research and Advance Engineering, Robert Bosch GmbH, Robert-Bosch-Campus 1, 71272, Renningen, Germany
| | - Christopher Johnson
- Robert Bosch Research & Technology Center, Robert Bosch LLC, 384 Santa Trinita Avenue, Sunnyvale, CA, 94085, USA
| | - Steffen Rupp
- Institute of Interfacial Process Engineering and Plasma Technology, University of Stuttgart, Nobelstraße 12, 70569, Stuttgart, Germany
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Nobelstr. 12, 70569, Stuttgart, Germany
| | - Christian Grumaz
- Corporate Sector Research and Advance Engineering, Robert Bosch GmbH, Robert-Bosch-Campus 1, 71272, Renningen, Germany.
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4
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Park SY, Faraci G, Ward P, Lee HY. Utilizing cost-effective portable equipment to enhance COVID-19 variant tracking both on-site and at a large scale. J Clin Microbiol 2024; 62:e0155823. [PMID: 38415638 PMCID: PMC11005371 DOI: 10.1128/jcm.01558-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
Despite optimistic predictions on the eventual end of COVID-19 (Coronavirus Disease 2019), caution is necessary regarding the emergence of new variants to sustain a positive outlook and effectively address any potential future outbreaks. However, ongoing efforts to track COVID-19 variants are concentrated in developed countries and unique social practices and remote habitats of indigenous peoples present additional challenges. By combining small-sized equipment that is easily accessible and inexpensive, we performed SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) whole genome sequencing and measured the sample-to-answer time and accuracy of this portable variant tracking tool. Our portable design determined the variant of SARS-CoV-2 in an infected individual within 9 hours and 15 minutes without external power or internet connection, surpassing the speed of previous portable tools. It took only 16 minutes to complete sequencing run, whole genome assembly, and lineage determination using a single standalone laptop. We then demonstrated the capability to produce 289 SARS-CoV-2 whole genome sequences in a single portable sequencing run, representing a significant improvement over an existing throughput of 96 sequences per run. We verified the accuracy of portable sequencing by comparison with two other independent sequencing methods. We showed that our high-throughput data consistently represented the circulating variants in Los Angeles, United States, when compared with publicly available sequences. Our scheme is designed to be flexible, rapid, and accurate, making it a valuable tool for large-scale surveillance operations in low- and middle-income countries as well as targeted surveys for vulnerable populations in remote locations.IMPORTANCEThere have been significant efforts to track COVID-19 (Coronavirus Disease 2019) variants, accumulating over 15 million SARS-CoV-2 sequences as of 2023. However, the distribution of global survey data is highly skewed, with nearly half of all countries having inadequate or low levels of genomic surveillance. In addition, indigenous peoples face more severe threats from COVID-19, due to their generally remote residence and unique social practices. Cost-effective portable sequencing tools have been used to investigate Ebola and Zika outbreaks. However, these tools have a sample-to-answer time of around 24 hours and require an internet connection for data transfer to an off-site cloud server. In our study, we rapidly determined COVID-19 variants using only small and inexpensive equipment, with a completion time of 9 hours and 15 minutes. Furthermore, we produced 289 near-full-length SARS-CoV-2 genome sequences from a single portable Nanopore sequencing run, representing a threefold increase in throughput compared with existing Nanopore sequencing methods.
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Affiliation(s)
- Sung Yong Park
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Gina Faraci
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Pamela Ward
- Department of Clinical Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Ha Youn Lee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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Gupta S, Singh B, Abhishek R, Gupta S, Sachan M. The emerging role of liquid biopsy in oral squamous cell carcinoma detection: advantages and challenges. Expert Rev Mol Diagn 2024; 24:311-331. [PMID: 38607339 DOI: 10.1080/14737159.2024.2340997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/05/2024] [Indexed: 04/13/2024]
Abstract
INTRODUCTION Oral Squamous Cell Carcinoma (OSCC), the sixth most widespread malignancy in the world, accounts for 90% of all cases of oral cancer. The primary risk factors are tobacco chewing, alcohol consumption, viral infection, and genetic modifications. OSCC has a high morbidity rate due to the lack of early diagnostic methods. Nowadays, liquid biopsy plays a vital role in the initial diagnosis of oral cancer. ctNAs extracted from saliva and serum/plasma offer meaningful insights into tumor genetics and dynamics. The interplay of these elements in saliva and serum/plasma showcases their significance in advancing noninvasive, effective OSCC detection and monitoring. AREAS COVERED This review mainly focused on the role of liquid biopsy as an emerging point in the diagnosis and prognosis of OSCC and the current advancements and challenges associated with liquid biopsy. EXPERT OPINION Liquid biopsy is regarded as a new, minimally invasive, real-time monitoring tool for cancer diagnosis and prognosis. Many biomolecules found in bodily fluids, including ctDNA, ctRNA, CTCs, and EVs, are significant biomarkers to identify cancer in its early stages. Despite these groundbreaking strides, challenges persist. Standardization of sample collection, isolation, processing, and detection methods is imperative for ensuring result reproducibility across diverse studies.
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Affiliation(s)
- Sudha Gupta
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, India
| | - Brijesh Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, India
| | - Rajul Abhishek
- Department of Surgical Oncology, Motilal Nehru Medical College, Prayagraj, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George Medical University, Lucknow, India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, India
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Lee S, Park JS, Woo H, Yoo YK, Lee D, Chung S, Yoon DS, Lee KB, Lee JH. Rapid deep learning-assisted predictive diagnostics for point-of-care testing. Nat Commun 2024; 15:1695. [PMID: 38402240 PMCID: PMC10894262 DOI: 10.1038/s41467-024-46069-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/12/2024] [Indexed: 02/26/2024] Open
Abstract
Prominent techniques such as real-time polymerase chain reaction (RT-PCR), enzyme-linked immunosorbent assay (ELISA), and rapid kits are currently being explored to both enhance sensitivity and reduce assay time for diagnostic tests. Existing commercial molecular methods typically take several hours, while immunoassays can range from several hours to tens of minutes. Rapid diagnostics are crucial in Point-of-Care Testing (POCT). We propose an approach that integrates a time-series deep learning architecture and AI-based verification, for the enhanced result analysis of lateral flow assays. This approach is applicable to both infectious diseases and non-infectious biomarkers. In blind tests using clinical samples, our method achieved diagnostic times as short as 2 minutes, exceeding the accuracy of human analysis at 15 minutes. Furthermore, our technique significantly reduces assay time to just 1-2 minutes in the POCT setting. This advancement has the potential to greatly enhance POCT diagnostics, enabling both healthcare professionals and non-experts to make rapid, accurate decisions.
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Affiliation(s)
- Seungmin Lee
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
- School of Biomedical Engineering, Korea University, 145 Anam-ro, Seongbuk, Seoul, 02841, Republic of Korea
| | - Jeong Soo Park
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
- School of Mechanical Engineering, Korea University, 145 Anam-ro, Seoungbuk-gu, Seoul, 02841, Republic of Korea
| | - Hyowon Woo
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
| | - Yong Kyoung Yoo
- Department of Electronic Engineering, Catholic Kwandong University, 24, Beomil-ro 579 beon-gil, Gangneung-si, Gangwon-do, 25601, Republic of Korea
| | - Dongho Lee
- CALTH Inc., Changeop-ro 54, Seongnam, Gyeonggi, 13449, Republic of Korea
| | - Seok Chung
- School of Mechanical Engineering, Korea University, 145 Anam-ro, Seoungbuk-gu, Seoul, 02841, Republic of Korea
| | - Dae Sung Yoon
- School of Biomedical Engineering, Korea University, 145 Anam-ro, Seongbuk, Seoul, 02841, Republic of Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, Republic of Korea
- Astrion Inc, Seoul, 02841, Republic of Korea
| | - Ki-Baek Lee
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
| | - Jeong Hoon Lee
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea.
- CALTH Inc., Changeop-ro 54, Seongnam, Gyeonggi, 13449, Republic of Korea.
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7
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Poret AJ, Schaefers M, Merakou C, Mansour KE, Lagoudas GK, Cross AR, Goldberg JB, Kishony R, Uluer AZ, McAdam AJ, Blainey PC, Vargas SO, Lieberman TD, Priebe GP. De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579193. [PMID: 38370793 PMCID: PMC10871308 DOI: 10.1101/2024.02.06.579193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Bacteria evolving within human hosts encounter selective tradeoffs that render mutations adaptive in one context and deleterious in another. Here, we report that the cystic fibrosis-associated pathogen Burkholderia dolosa overcomes in-human selective tradeoffs by acquiring successive point mutations that alternate phenotypes. We sequenced the whole genomes of 931 respiratory isolates from two recently infected patients and an epidemiologically-linked, chronically-infected patient. These isolates are contextualized using 112 historical genomes from the same outbreak strain. Within both newly infected patients, diverse parallel mutations that disrupt O-antigen expression quickly arose, comprising 29% and 63% of their B. dolosa communities by 3 years. The selection for loss of O-antigen starkly contrasts with our previous observation of parallel O-antigen-restoring mutations after many years of chronic infection in the historical outbreak. Experimental characterization revealed that O-antigen loss increases uptake in immune cells while decreasing competitiveness in the mouse lung. We propose that the balance of these pressures, and thus whether O-antigen expression is advantageous, depends on tissue localization and infection duration. These results suggest that mutation-driven alternation during infection may be more frequent than appreciated and is underestimated without dense temporal sampling.
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Affiliation(s)
- Alexandra J. Poret
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology
- Department of Biological Engineering, Massachusetts Institute of Technology
| | - Matthew Schaefers
- Department of Anesthesiology, Critical Care and Pain Medicine, Division of Critical Care Medicine, Boston Children's Hospital
- Department of Anaesthesia, Harvard Medical School, Boston, Massachusetts
| | - Christina Merakou
- Department of Anesthesiology, Critical Care and Pain Medicine, Division of Critical Care Medicine, Boston Children's Hospital
- Department of Anaesthesia, Harvard Medical School, Boston, Massachusetts
| | - Kathryn E. Mansour
- Department of Anesthesiology, Critical Care and Pain Medicine, Division of Critical Care Medicine, Boston Children's Hospital
| | - Georgia K. Lagoudas
- Department of Biological Engineering, Massachusetts Institute of Technology
- Broad Institute of MIT and Harvard
| | - Ashley R. Cross
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine
| | - Joanna B. Goldberg
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine
| | - Roy Kishony
- Faculty of Biology and Faculty of Computer Science, Technion Israel
| | - Ahmet Z. Uluer
- Department of Pediatrics, Division of Respiratory Diseases, Boston Children’s Hospital
- Adult CF Program, Brigham and Women’s Hospital
- Department of Pediatrics, Harvard Medical School
| | - Alexander J. McAdam
- Department of Laboratory Medicine, Boston Children’s Hospital
- Department of Pathology, Harvard Medical School
| | - Paul C. Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology
- Broad Institute of MIT and Harvard
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
| | - Sara O. Vargas
- Department of Pathology, Harvard Medical School
- Department of Pathology, Boston Children’s Hospital
| | - Tami D. Lieberman
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology
- Department of Anesthesiology, Critical Care and Pain Medicine, Division of Critical Care Medicine, Boston Children's Hospital
| | - Gregory P. Priebe
- Department of Anesthesiology, Critical Care and Pain Medicine, Division of Critical Care Medicine, Boston Children's Hospital
- Department of Anaesthesia, Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard
- Department of Pediatrics, Division of Infectious Diseases, Boston Children’s Hospital
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8
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Guo J, Brassard D, Adam N, Verster AJ, Shay JA, Miville-Godin C, Janta-Polczynski M, Ferreira J, Mounier M, Pilar AV, Tapp K, Classen A, Shiu M, Charlebois D, Petronella N, Weedmark K, Corneau N, Veres T. Automated centrifugal microfluidic system for the preparation of adaptor-ligated sequencing libraries. LAB ON A CHIP 2024; 24:182-196. [PMID: 38044704 DOI: 10.1039/d3lc00781b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The intensive workload associated with the preparation of high-quality DNA libraries remains a key obstacle toward widespread deployment of sequencing technologies in remote and resource-limited areas. We describe the development of single-use microfluidic devices driven by an advanced pneumatic centrifugal microfluidic platform, the PowerBlade, to automate the preparation of Illumina-compatible libraries based on adaptor ligation methodology. The developed on-chip workflow includes enzymatic DNA fragmentation coupled to end-repair, adaptor ligation, first DNA cleanup, PCR amplification, and second DNA cleanup. This complex workflow was successfully integrated into simple thermoplastic microfluidic devices that are amenable to mass production with injection molding. The system was validated by preparing, on chip, libraries from a mixture of genomic DNA extracted from three common foodborne pathogens (Listeria monocytogenes, Escherichia coli and Salmonella enterica serovar Typhimurium) and comparing them with libraries made via a manual procedure. The two types of libraries were found to exhibit similar quality control metrics (including genome coverage, assembly, and relative abundances) and led to nearly uniform coverage independent of GC content. This microfluidic technology offers a time-saving and cost-effective alternative to manual procedures and robotic-based automation, making it suitable for deployment in remote environments where technical expertise and resources might be scarce. Specifically, it facilitates field practices that involve mid- to low-throughput sequencing, such as tasks related to foodborne pathogen detection, characterization, and microbial profiling.
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Affiliation(s)
- Jimin Guo
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Daniel Brassard
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Nadine Adam
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Adrian J Verster
- Bureau of Food Surveillance and Science Integration, Bioinformatics High-Capacity Computing Laboratory, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Julie A Shay
- Bureau of Food Surveillance and Science Integration, Bioinformatics High-Capacity Computing Laboratory, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Caroline Miville-Godin
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Mojra Janta-Polczynski
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Jason Ferreira
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Maxence Mounier
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Ana V Pilar
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Kyle Tapp
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Adam Classen
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Matthew Shiu
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Denis Charlebois
- Canadian Space Agency, 6767 Route de l'Aéroport, Saint-Hubert, QC J3Y 8Y9, Canada
| | - Nicholas Petronella
- Bureau of Food Surveillance and Science Integration, Bioinformatics High-Capacity Computing Laboratory, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Kelly Weedmark
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Nathalie Corneau
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Teodor Veres
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
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9
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Stephenson A, Lastra L, Nguyen B, Chen YJ, Nivala J, Ceze L, Strauss K. Physical Laboratory Automation in Synthetic Biology. ACS Synth Biol 2023; 12:3156-3169. [PMID: 37935025 DOI: 10.1021/acssynbio.3c00345] [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] [Indexed: 11/09/2023]
Abstract
Synthetic Biology has overcome many of the early challenges facing the field and is entering a systems era characterized by adoption of Design-Build-Test-Learn (DBTL) approaches. The need for automation and standardization to enable reproducible, scalable, and translatable research has become increasingly accepted in recent years, and many of the hardware and software tools needed to address these challenges are now in place or under development. However, the lack of connectivity between DBTL modules and barriers to access and adoption remain significant challenges to realizing the full potential of lab automation. In this review, we characterize and classify the state of automation in synthetic biology with a focus on the physical automation of experimental workflows. Though fully autonomous scientific discovery is likely a long way off, impressive progress has been made toward automating critical elements of experimentation by combining intelligent hardware and software tools. It is worth questioning whether total automation that removes humans entirely from the loop should be the ultimate goal, and considerations for appropriate automation versus total automation are discussed in this light while emphasizing areas where further development is needed in both contexts.
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Affiliation(s)
- Ashley Stephenson
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
- Microsoft Research, Redmond, Washington 98052, United States
| | - Lauren Lastra
- Microsoft Research, Redmond, Washington 98052, United States
| | - Bichlien Nguyen
- Microsoft Research, Redmond, Washington 98052, United States
| | - Yuan-Jyue Chen
- Microsoft Research, Redmond, Washington 98052, United States
| | - Jeff Nivala
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Luis Ceze
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Karin Strauss
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
- Microsoft Research, Redmond, Washington 98052, United States
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10
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Ismail N, Dippenaar A, Morgan G, Grobbelaar M, Wells F, Caffry J, Morais C, Gizynski K, McGurk D, Boada E, Murton H, Warren RM, Van Rie A. Microfluidic Capture of Mycobacterium tuberculosis from Clinical Samples for Culture-Free Whole-Genome Sequencing. Microbiol Spectr 2023; 11:e0111423. [PMID: 37358439 PMCID: PMC10433858 DOI: 10.1128/spectrum.01114-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/25/2023] [Indexed: 06/27/2023] Open
Abstract
Mycobacterium tuberculosis whole-genome sequencing (WGS) is a powerful tool as it can provide data on population diversity, drug resistance, disease transmission, and mixed infections. Successful WGS is still reliant on high concentrations of DNA obtained through M. tuberculosis culture. Microfluidics technology plays a valuable role in single-cell research but has not yet been assessed as a bacterial enrichment strategy for culture-free WGS of M. tuberculosis. In a proof-of-principle study, we evaluated the use of Capture-XT, a microfluidic lab-on-chip cleanup and pathogen concentration platform to enrich M. tuberculosis bacilli from clinical sputum specimens for downstream DNA extraction and WGS. Three of the four (75%) samples processed by the microfluidics application passed the library preparation quality control, compared to only one of the four (25%) samples not enriched by the microfluidics M. tuberculosis capture application. WGS data were of sufficient quality, with mapping depth of ≥25× and 9 to 27% of reads mapping to the reference genome. These results suggest that microfluidics-based M. tuberculosis cell capture might be a promising method for M. tuberculosis enrichment in clinical sputum samples, which could facilitate culture-free M. tuberculosis WGS. IMPORTANCE Diagnosis of tuberculosis is effective using molecular methods; however, a comprehensive characterization of the resistance profile of Mycobacterium tuberculosis often requires culturing and phenotypic drug susceptibility testing or culturing followed by whole-genome sequencing (WGS). The phenotypic route can take anywhere from 1 to >3 months to result, by which point the patient may have acquired additional drug resistance. The WGS route is a very attractive option; however, culturing is the rate-limiting step. In this original article, we provide proof-of-principle evidence that microfluidics-based cell capture can be used on high-bacillary-load clinical samples for culture-free WGS.
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Affiliation(s)
- Nabila Ismail
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Anzaan Dippenaar
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Melanie Grobbelaar
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Felicia Wells
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | | | | | | | - David McGurk
- QuantuMDx Ltd., Newcastle upon Tyne, United Kingdom
| | | | | | - Robin M. Warren
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Annelies Van Rie
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
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11
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Wu X, Tang D, He Q, Liu L, Jia Z, Tan Y. Research progress of electrode shapes in EWOD-based digital microfluidics. RSC Adv 2023; 13:16815-16827. [PMID: 37283873 PMCID: PMC10240258 DOI: 10.1039/d3ra01817b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/25/2023] [Indexed: 06/08/2023] Open
Abstract
Digital microfluidics (DMF) is an innovative technology used for precise manipulation of liquid droplets. This technology has garnered significant attention in both industrial applications and scientific research due to its unique advantages. Among the key components of DMF, the driving electrode plays a role in facilitating droplet generation, transportation, splitting, merging, and mixing. This comprehensive review aims to present an in-depth understanding of the working principle of DMF particularly focusing on the Electrowetting On Dielectric (EWOD) method. Furthermore, it examines the impact of driving electrodes with varying geometries on droplet manipulation. By analyzing and comparing their characteristics, this review offers valuable insights and a fresh perspective on the design and application of driving electrodes in DMF based on the EWOD approach. Lastly, an assessment of the development trend and potential applications of DMF concludes the review, providing an outlook for future prospects in the field.
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Affiliation(s)
- Xingyue Wu
- School of Electrical Engineering, Ultra-fast/Micro-nano Technology and Advanced Laser Manufacturing Key Laboratory of Hunan Province, University of South China Hengyang 421001 China
| | - Dongbao Tang
- School of Electrical Engineering, Ultra-fast/Micro-nano Technology and Advanced Laser Manufacturing Key Laboratory of Hunan Province, University of South China Hengyang 421001 China
| | - Qianpei He
- Department of Comparative Medicine, School of Medicine, University of Washington Seattle WA USA
| | - Luxuan Liu
- School of Electrical Engineering, Ultra-fast/Micro-nano Technology and Advanced Laser Manufacturing Key Laboratory of Hunan Province, University of South China Hengyang 421001 China
| | - Zhaoyuan Jia
- School of Electrical Engineering, Ultra-fast/Micro-nano Technology and Advanced Laser Manufacturing Key Laboratory of Hunan Province, University of South China Hengyang 421001 China
| | - Yuyu Tan
- School of Electrical Engineering, Ultra-fast/Micro-nano Technology and Advanced Laser Manufacturing Key Laboratory of Hunan Province, University of South China Hengyang 421001 China
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12
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de Olazarra AS, Wang SX. Advances in point-of-care genetic testing for personalized medicine applications. BIOMICROFLUIDICS 2023; 17:031501. [PMID: 37159750 PMCID: PMC10163839 DOI: 10.1063/5.0143311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Breakthroughs within the fields of genomics and bioinformatics have enabled the identification of numerous genetic biomarkers that reflect an individual's disease susceptibility, disease progression, and therapy responsiveness. The personalized medicine paradigm capitalizes on these breakthroughs by utilizing an individual's genetic profile to guide treatment selection, dosing, and preventative care. However, integration of personalized medicine into routine clinical practice has been limited-in part-by a dearth of widely deployable, timely, and cost-effective genetic analysis tools. Fortunately, the last several decades have been characterized by tremendous progress with respect to the development of molecular point-of-care tests (POCTs). Advances in microfluidic technologies, accompanied by improvements and innovations in amplification methods, have opened new doors to health monitoring at the point-of-care. While many of these technologies were developed with rapid infectious disease diagnostics in mind, they are well-suited for deployment as genetic testing platforms for personalized medicine applications. In the coming years, we expect that these innovations in molecular POCT technology will play a critical role in enabling widespread adoption of personalized medicine methods. In this work, we review the current and emerging generations of point-of-care molecular testing platforms and assess their applicability toward accelerating the personalized medicine paradigm.
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Affiliation(s)
- A. S. de Olazarra
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
| | - S. X. Wang
- Author to whom correspondence should be addressed:
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13
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Luo Y, Cao Z, Liu Y, Zhang R, Yang S, Wang N, Shi Q, Li J, Dong S, Fan C, Zhao J. The emerging landscape of microfluidic applications in DNA data storage. LAB ON A CHIP 2023; 23:1981-2004. [PMID: 36946437 DOI: 10.1039/d2lc00972b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
DNA has been considered a promising alternative to the current solid-state devices for digital information storage. The past decade has witnessed tremendous progress in the field of DNA data storage contributed by researchers from various disciplines. However, the current development status of DNA storage is still far from practical use, mainly due to its high material cost and time consumption for data reading/writing, as well as the lack of a comprehensive, automated, and integrated system. Microfluidics, being capable of handling and processing micro-scale fluid samples in a massively paralleled and highly integrated manner, has gradually been recognized as a promising candidate for addressing the aforementioned issues. In this review, we provide a discussion on recent efforts of applying microfluidics to advance the development of DNA data storage. Moreover, to showcase the tremendous potential that microfluidics can contribute to this field, we will further highlight the recent advancements of applying microfluidics to the key functional modules within the DNA data storage workflow. Finally, we share our perspectives on future directions for how to continue the infusion of microfluidics with DNA data storage and how to advance toward a truly integrated system and reach real-life applications.
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Affiliation(s)
- Yuan Luo
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Cao
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, China.
- International Joint Innovation Center, Zhejiang University, Haining 314400, China
| | - Yifan Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China
| | - Rong Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Shijia Yang
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Wang
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingyuan Shi
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Jie Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Shurong Dong
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, China.
- International Joint Innovation Center, Zhejiang University, Haining 314400, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianlong Zhao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, P.R. China
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14
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Development and clinical applications of an enclosed automated targeted NGS library preparation system. Clin Chim Acta 2023; 540:117224. [PMID: 36627008 DOI: 10.1016/j.cca.2023.117224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/09/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
The rapid development of next-generation sequencing (NGS) technology has promoted its wide clinical application in precision medicine for oncology. However, laborious and time-consuming manual operations, highly skilled personnel requirements, and cross-contamination are major challenges for the clinical implementation of NGS technology-based tests. The Automated NGS Diagnostic Solutions (ANDiS) 500 system is a fully enclosed cassette-dependent automated NGS library preparation system. This platform could produce qualified targeted amplicon library in three steps with only 15 min of hands-on time. Rigorous cross-contamination test using simulated contaminant plasmids confirmed that the design of disposable cassette guarantees zero sample cross-contamination. The BRCA1 and BRCA2 mutation detection panel and gastrointestinal cancer-related gene analysis panel for the ANDiS 500 platform showed 100% accuracy and precision in detecting germ-line mutations and somatic mutations respectively. Furthermore, those panels showed 100% concordance with verified methods in a prospective cohort study enrolling 363 patients and a cohort of 45 pan-cancer samples. In conclusion, the ANDiS 500 automated platform could overcome major challenges for implementing NGS assays clinically and is eligible for routine clinical tests.
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15
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Gonzalez-Suarez AM, Long A, Huang X, Revzin A. A Compact Control System to Enable Automated Operation of Microfluidic Bioanalytical Assays. BIOSENSORS 2022; 12:1160. [PMID: 36551127 PMCID: PMC9775492 DOI: 10.3390/bios12121160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 06/17/2023]
Abstract
We describe a control system for operating valve-enabled microfluidic devices and leverage this control system to carry out a complex workflow of plasma separation from 8 μL of whole blood followed by on-chip mixing of plasma with assay reagents for biomarker detection. The control system incorporates pumps, digital pressure sensors, a microcontroller, solenoid valves and off-the-shelf components to deliver high and low air pressure in the desired temporal sequence to meter fluid flow and actuate microvalves. Importantly, our control system is portable, which is suitable for operating the microvalve-enabled microfluidic devices in the point-of-care setting.
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Affiliation(s)
| | - Alexander Long
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biology, St. Olaf College, Northfield, MN 55057, USA
| | - XuHai Huang
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Alexander Revzin
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
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16
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Zare Harofte S, Soltani M, Siavashy S, Raahemifar K. Recent Advances of Utilizing Artificial Intelligence in Lab on a Chip for Diagnosis and Treatment. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2203169. [PMID: 36026569 DOI: 10.1002/smll.202203169] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/16/2022] [Indexed: 05/14/2023]
Abstract
Nowadays, artificial intelligence (AI) creates numerous promising opportunities in the life sciences. AI methods can be significantly advantageous for analyzing the massive datasets provided by biotechnology systems for biological and biomedical applications. Microfluidics, with the developments in controlled reaction chambers, high-throughput arrays, and positioning systems, generate big data that is not necessarily analyzed successfully. Integrating AI and microfluidics can pave the way for both experimental and analytical throughputs in biotechnology research. Microfluidics enhances the experimental methods and reduces the cost and scale, while AI methods significantly improve the analysis of huge datasets obtained from high-throughput and multiplexed microfluidics. This review briefly presents a survey of the role of AI and microfluidics in biotechnology. Also, the incorporation of AI with microfluidics is comprehensively investigated. Specifically, recent studies that perform flow cytometry cell classification, cell isolation, and a combination of them by gaining from both AI methods and microfluidic techniques are covered. Despite all current challenges, various fields of biotechnology can be remarkably affected by the combination of AI and microfluidic technologies. Some of these fields include point-of-care systems, precision, personalized medicine, regenerative medicine, prognostics, diagnostics, and treatment of oncology and non-oncology-related diseases.
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Affiliation(s)
- Samaneh Zare Harofte
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, 19967-15433, Iran
| | - Madjid Soltani
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, 19967-15433, Iran
- Department of Electrical and Computer Engineering, Faculty of Engineering, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
- Centre for Biotechnology and Bioengineering (CBB), University of Waterloo, Waterloo, ON, N2L 3G1, Canada
- Advanced Bioengineering Initiative Center, Multidisciplinary International Complex, K. N. Toosi University of Technology, Tehran, 14176-14411, Iran
- Cancer Biology Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, 14197-33141, Iran
| | - Saeed Siavashy
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, 19967-15433, Iran
| | - Kaamran Raahemifar
- Data Science and Artificial Intelligence Program, College of Information Sciences and Technology (IST), Penn State University, State College, PA, 16801, USA
- School of Optometry and Vision Science, Faculty of Science, University of Waterloo, 200 University Ave. W, Waterloo, ON, N2L 3G1, Canada
- Department of Chemical Engineering, Faculty of Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON, N2L 3G1, Canada
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17
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Luo Y, Wang S, Feng Z, Li J, Mao C, Wang R, Jiang X. Integrated Microfluidic DNA Storage Platform with Automated Sample Handling and Physical Data Partitioning. Anal Chem 2022; 94:13153-13162. [DOI: 10.1021/acs.analchem.2c02667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuan Luo
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, No 1088, Xueyuan Rd., Xili, Nanshan
District, Shenzhen518055, Guangdong, P. R. China
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai200050, China
| | - Shuchen Wang
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, No 1088, Xueyuan Rd., Xili, Nanshan
District, Shenzhen518055, Guangdong, P. R. China
| | - Zhuowei Feng
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, No 1088, Xueyuan Rd., Xili, Nanshan
District, Shenzhen518055, Guangdong, P. R. China
| | - Jie Li
- Department of Electronic and Electrical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
| | - Cuiping Mao
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, No 1088, Xueyuan Rd., Xili, Nanshan
District, Shenzhen518055, Guangdong, P. R. China
| | - Rui Wang
- Department of Electronic and Electrical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
| | - Xingyu Jiang
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, No 1088, Xueyuan Rd., Xili, Nanshan
District, Shenzhen518055, Guangdong, P. R. China
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18
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Yin J, Chen X, Li X, Kang G, Wang P, Song Y, Ijaz UZ, Yin H, Huang H. A droplet-based microfluidic approach to isolating functional bacteria from gut microbiota. Front Cell Infect Microbiol 2022; 12:920986. [PMID: 36061857 PMCID: PMC9433703 DOI: 10.3389/fcimb.2022.920986] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 08/01/2022] [Indexed: 12/05/2022] Open
Abstract
Metabolic interactions within gut microbiota play a vital role in human health and disease. Targeting metabolically interacting bacteria could provide effective treatments; however, obtaining functional bacteria remains a significant challenge due to the complexity of gut microbiota. Here, we developed a facile droplet-based approach to isolate and enrich functional gut bacteria that could utilize metabolites from an engineered butyrate-producing bacteria (EBPB) of anti-obesity potential. This involves the high throughput formation of single-bacteria droplets, followed by culturing “droplets” on agar plates to form discrete single-cell colonies. This approach eliminates the need for sophisticated s instruments to sort droplets and thus allows the operation hosted in a traditional anaerobic chamber. In comparison to the traditional culture, the droplet-based approach obtained a community of substantially higher diversity and evenness. Using the conditioned plates containing metabolites from the EBPB supernatant, we obtained gut bacteria closely associated or interacting with the EBPB. These include anaerobic Lactobacillus and Bifidobacterium, which are often used as probiotics. The study illustrates the potential of our approach in the search for the associated bacteria within the gut microbiota and retrieving those yet-to-be cultured.
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Affiliation(s)
- Jianan Yin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontiers Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xiuzhao Chen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontiers Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xiaobo Li
- New Technology R & D Department, Tianjin Modern Innovative TCM Technology Co. Ltd., Tianjin, China
| | - Guangbo Kang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontiers Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Institute of Shaoxing, Tianjin University, Zhejiang, China
| | - Ping Wang
- New Technology R & D Department, Tianjin Modern Innovative TCM Technology Co. Ltd., Tianjin, China
| | - Yanqing Song
- James Watt School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Umer Zeeshan Ijaz
- James Watt School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Huabing Yin
- James Watt School of Engineering, University of Glasgow, Glasgow, United Kingdom
- *Correspondence: Huabing Yin, ; He Huang,
| | - He Huang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontiers Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- *Correspondence: Huabing Yin, ; He Huang,
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19
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Sinha N, Yang H, Janse D, Hendriks L, Rand U, Hauser H, Köster M, van de Vosse FN, de Greef TFA, Tel J. Microfluidic chip for precise trapping of single cells and temporal analysis of signaling dynamics. COMMUNICATIONS ENGINEERING 2022; 1:18. [PMCID: PMC10955935 DOI: 10.1038/s44172-022-00019-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2024]
Abstract
Microfluidic designs are versatile examples of technology miniaturisation that find their applications in various cell biology research, especially to investigate the influence of environmental signals on cellular response dynamics. Multicellular systems operate in intricate cellular microenvironments where environmental signals govern well-orchestrated and robust responses, the understanding of which can be realized with integrated microfluidic systems. In this study, we present a fully automated and integrated microfluidic chip that can deliver input signals to single and isolated suspension or adherent cells in a precisely controlled manner. In respective analyses of different single cell types, we observe, in real-time, the temporal dynamics of caspase 3 activation during DMSO-induced apoptosis in single cancer cells (K562) and the translocation of STAT-1 triggered by interferon γ (IFNγ) in single fibroblasts (NIH3T3). Our investigations establish the employment of our versatile microfluidic system in probing temporal single cell signaling networks where alternations in outputs uncover signal processing mechanisms. Nidhi Sinha, Haowen Yang and colleagues report a microfluidic large-scale integration chip to probe temporal single-cell signalling networks via the delivery of patterns of input signalling molecules. The researchers use their device to investigate drug-induced cancer cell apoptosis and single cell transcription (STAT-1) protein signalling dynamics.
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Affiliation(s)
- Nidhi Sinha
- Laboratory of Immunoengineering, Department of Biomedical Engineering, TU Eindhoven, 5600 MB Eindhoven, Netherlands
- Institute of Complex Molecular Systems, TU Eindhoven, 5600 MB Eindhoven, Netherlands
| | - Haowen Yang
- Laboratory of Immunoengineering, Department of Biomedical Engineering, TU Eindhoven, 5600 MB Eindhoven, Netherlands
- Institute of Complex Molecular Systems, TU Eindhoven, 5600 MB Eindhoven, Netherlands
| | - David Janse
- Laboratory of Immunoengineering, Department of Biomedical Engineering, TU Eindhoven, 5600 MB Eindhoven, Netherlands
| | - Luc Hendriks
- Laboratory of Immunoengineering, Department of Biomedical Engineering, TU Eindhoven, 5600 MB Eindhoven, Netherlands
| | - Ulfert Rand
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Hansjörg Hauser
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Mario Köster
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Frans N. van de Vosse
- Cardiovascular Biomechanics Group, Department of Biomedical Engineering, TU Eindhoven, 5600 MB Eindhoven, Netherlands
| | - Tom F. A. de Greef
- Institute of Complex Molecular Systems, TU Eindhoven, 5600 MB Eindhoven, Netherlands
- Computational Biology Group, Department of Biomedical Engineering, TU Eindhoven, 5600 MB Eindhoven, Netherlands
| | - Jurjen Tel
- Laboratory of Immunoengineering, Department of Biomedical Engineering, TU Eindhoven, 5600 MB Eindhoven, Netherlands
- Institute of Complex Molecular Systems, TU Eindhoven, 5600 MB Eindhoven, Netherlands
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20
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Akther F, Zhang J, Tran HDN, Fallahi H, Adelnia H, Phan HP, Nguyen NT, Ta HT. Atherothrombosis-on-Chip: A Site-Specific Microfluidic Model for Thrombus Formation and Drug Discovery. Adv Biol (Weinh) 2022; 6:e2101316. [PMID: 35666057 DOI: 10.1002/adbi.202101316] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/06/2022] [Indexed: 01/28/2023]
Abstract
Atherothrombosis, an atherosclerotic plaque disruption condition with superimposed thrombosis, is the underlying cause of cardiovascular episodes. Herein, a unique design is presented to develop a microfluidic site-specific atherothrombosis-on-chip model, providing a universal platform for studying the crosstalk between blood cells and plaque components. The device consists of two interconnected microchannels, namely main and supporting channels: the former mimics the vessel geometry with different stenosis, and the latter introduces plaque components to the circulation simultaneously. The unique design allows the site-specific introduction of plaque components in stenosed channels ranging from 0% to above 50%, resulting in thrombosis, which has not been achieved previously. The device successfully explains the correlation between vessel geometry and thrombus formation phenomenon as well as the influence of shear rate on platelet aggregation, confirming the reliability and the effectiveness of the design. The device exhibits significant sensitivity to aspirin. In therapeutic doses (50 × 10-6 and 100 × 10-6 m), aspirin delays and prevents platelet adhesion, thereby reducing the thrombus area in a dose-dependent manner. Finally, the device is effectively employed in testing the targeted binding of the RGD (arginyl-glycyl-aspartic acid) labeled polymeric nanoparticles on the thrombus, extending the use of the device to examine targeted drug carriers.
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Affiliation(s)
- Fahima Akther
- Queensland Micro- and Nanotechnology, Griffith University, Nathan, Queensland, 4111, Australia.,Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Jun Zhang
- Queensland Micro- and Nanotechnology, Griffith University, Nathan, Queensland, 4111, Australia
| | - Huong D N Tran
- Queensland Micro- and Nanotechnology, Griffith University, Nathan, Queensland, 4111, Australia.,Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Hedieh Fallahi
- Queensland Micro- and Nanotechnology, Griffith University, Nathan, Queensland, 4111, Australia
| | - Hossein Adelnia
- Queensland Micro- and Nanotechnology, Griffith University, Nathan, Queensland, 4111, Australia.,Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Hoang-Phuong Phan
- Queensland Micro- and Nanotechnology, Griffith University, Nathan, Queensland, 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology, Griffith University, Nathan, Queensland, 4111, Australia
| | - Hang Thu Ta
- Queensland Micro- and Nanotechnology, Griffith University, Nathan, Queensland, 4111, Australia.,Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Queensland, 4072, Australia.,School of Environment and Science, Griffith University, Nathan, Queensland, 4111, Australia
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21
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Target Enrichment Approaches for Next-Generation Sequencing Applications in Oncology. Diagnostics (Basel) 2022; 12:diagnostics12071539. [PMID: 35885445 PMCID: PMC9318977 DOI: 10.3390/diagnostics12071539] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/29/2022] Open
Abstract
Screening for genomic sequence variants in genes of predictive and prognostic significance is an integral part of precision medicine. Next-generation sequencing (NGS) technologies are progressively becoming platforms of choice to facilitate this, owing to their massively parallel sequencing capability, which can be used to simultaneously screen multiple markers in multiple samples for a variety of variants (single nucleotide and multi nucleotide variants, insertions and deletions, gene copy number variations, and fusions). A crucial step in the workflow of targeted NGS is the enrichment of the genomic regions of interest to be sequenced, against the whole genomic background. This ensures that the NGS effort is focused to predominantly screen target regions of interest with minimal off-target sequencing, making it more accurate and economical. Polymerase chain reaction-based (PCR, or amplicon-based) and hybridization capture-based methodologies are the two prominent approaches employed for target enrichment. This review summarizes the basic principles of target enrichment utilized by these methods, their multiple variations that have evolved over time, automation approaches, overall comparison of their advantages and drawbacks, and commercially available choices for these methodologies.
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22
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Liu Y, Jeraldo P, Herbert W, McDonough S, Eckloff B, Schulze-Makuch D, de Vera JP, Cockell C, Leya T, Baqué M, Jen J, Walther-Antonio M. Whole genome sequencing of cyanobacterium Nostoc sp. CCCryo 231-06 using microfluidic single cell technology. iScience 2022; 25:104291. [PMID: 35573199 PMCID: PMC9095746 DOI: 10.1016/j.isci.2022.104291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/16/2022] [Accepted: 04/20/2022] [Indexed: 11/26/2022] Open
Abstract
The Nostoc sp. strain CCCryo 231-06 is a cyanobacterial strain capable of surviving under extreme conditions and thus is of great interest for the astrobiology community. The knowledge of its complete genome sequence would serve as a guide for further studies. However, a major concern has been placed on the effects of contamination on the quality of sequencing data without a reference genome. Here, we report the use of microfluidic technology combined with single cell sequencing and de novo assembly to minimize the contamination and recover the complete genome of the Nostoc strain CCCryo 231-06 with high quality. 100% of the whole genome was recovered with all contaminants removed and a strongly supported phylogenetic tree. The data reported can be useful for comparative genomics for phylogenetic and taxonomic studies. The method used in this work can be applied to studies that require high-quality assemblies of genomes of unknown microorganisms. This work uses a microfluidic platform for Nostoc single cell sequencing This technology provides minimal contamination in single cell sequencing Complete genome of the Nostoc strain CCCryo 231-06 was recovered with high quality
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23
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Zhu X, Wang K, Yan H, Liu C, Zhu X, Chen B. Microfluidics as an Emerging Platform for Exploring Soil Environmental Processes: A Critical Review. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:711-731. [PMID: 34985862 DOI: 10.1021/acs.est.1c03899] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Investigating environmental processes, especially those occurring in soils, calls for innovative and multidisciplinary technologies that can provide insights at the microscale. The heterogeneity, opacity, and dynamics make the soil a "black box" where interactions and processes are elusive. Recently, microfluidics has emerged as a powerful research platform and experimental tool which can create artificial soil micromodels, enabling exploring soil processes on a chip. Micro/nanofabricated microfluidic devices can mimic some of the key features of soil with highly controlled physical and chemical microenvironments at the scale of pores, aggregates, and microbes. The combination of various techniques makes microfluidics an integrated approach for observation, reaction, analysis, and characterization. In this review, we systematically summarize the emerging applications of microfluidic soil platforms, from investigating soil interfacial processes and soil microbial processes to soil analysis and high-throughput screening. We highlight how innovative microfluidic devices are used to provide new insights into soil processes, mechanisms, and effects at the microscale, which contribute to an integrated interrogation of the soil systems across different scales. Critical discussions of the practical limitations of microfluidic soil platforms and perspectives of future research directions are summarized. We envisage that microfluidics will represent the technological advances toward microscopic, controllable, and in situ soil research.
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Affiliation(s)
- Xiangyu Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Kun Wang
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Huicong Yan
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Congcong Liu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Xiaoying Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Baoliang Chen
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
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24
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Vandghanooni S, Sanaat Z, Farahzadi R, Eskandani M, Omidian H, Omidi Y. Recent progress in the development of aptasensors for cancer diagnosis: Focusing on aptamers against cancer biomarkers. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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25
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Hess JF, Hess ME, Zengerle R, Paust N, Boerries M, Hutzenlaub T. Automated library preparation for whole genome sequencing by centrifugal microfluidics. Anal Chim Acta 2021; 1182:338954. [PMID: 34602197 DOI: 10.1016/j.aca.2021.338954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 07/19/2021] [Accepted: 08/02/2021] [Indexed: 11/18/2022]
Abstract
Next generation sequencing is evolving from a research tool into a method applied in diagnostic routine. The complete sequencing workflow includes sample pre-processing, library preparation, sequencing and bioinformatics. High quality in each of these steps is necessary to obtain excellent sequencing results. The tedious and error-prone library preparation poses a significant challenge for smaller laboratories, where high throughput pipetting robots are not cost-effective. Here we present an automated library preparation for whole genome sequencing using centrifugal microfluidics. Two samples can be run per cartridge. Precise metering of reagents allows the required liquid volumes to be reduced by 40% and the amount of sample used by 60%. The functionality of the cartridge is demonstrated with bacteria and DNA extracted from a human FFPE sample. For the bacterial sample, mean sequencing depths from 140 to 183 reads and a coverage of 99.8% of the reference genome were detected. For the human DNA, mean sequencing depths of 4.4-5.7 reads and a coverage of 78.2% of the effective reference genome were observed.
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Affiliation(s)
- Jacob Friedrich Hess
- Laboratory for MEMS Applications, IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110, Freiburg, Germany; Hahn-Schickard, Georges-Koehler-Allee 103, 79110, Freiburg, Germany.
| | - Maria Elena Hess
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacherstr. 153, 79110, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Roland Zengerle
- Laboratory for MEMS Applications, IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110, Freiburg, Germany; Hahn-Schickard, Georges-Koehler-Allee 103, 79110, Freiburg, Germany
| | - Nils Paust
- Laboratory for MEMS Applications, IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110, Freiburg, Germany; Hahn-Schickard, Georges-Koehler-Allee 103, 79110, Freiburg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacherstr. 153, 79110, Freiburg, Germany; German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tobias Hutzenlaub
- Laboratory for MEMS Applications, IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110, Freiburg, Germany; Hahn-Schickard, Georges-Koehler-Allee 103, 79110, Freiburg, Germany
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26
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Cahn JKB, Piel J. Anwendungen von Einzelzellmethoden in der mikrobiellen Naturstoffforschung. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.201900532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jackson K. B. Cahn
- Institut für Mikrobiologie Eidgenössische Technische Hochschule Zürich (ETH) 8093 Zürich Schweiz
| | - Jörn Piel
- Institut für Mikrobiologie Eidgenössische Technische Hochschule Zürich (ETH) 8093 Zürich Schweiz
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27
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Sharma S, Bhatia V. Magnetic nanoparticles in microfluidics-based diagnostics: an appraisal. Nanomedicine (Lond) 2021; 16:1329-1342. [PMID: 34027677 DOI: 10.2217/nnm-2021-0007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The use of magnetic nanoparticles (MNPs) in microfluidics based diagnostics is a classic case of micro-, nano- and bio-technology coming together to design extremely controllable, reproducible, and scalable nano and micro 'on-chip bio sensing systems.' In this review, applications of MNPs in microfluidics ranging from molecular diagnostics and immunodiagnostics to clinical uses have been examined. In addition, microfluidic mixing and capture of analytes using MNPs, and MNPs as carriers in microfluidic devices has been investigated. Finally, the challenges and future directions of this upcoming field have been summarized. The use of MNP-based microfluidic devices, will help in developing decentralized or 'point of care' testing globally, contributing to affordable healthcare, particularly, for middle- and low-income developing countries.
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Affiliation(s)
- Smriti Sharma
- Department of Chemistry, Miranda House, University of Delhi, India
| | - Vinayak Bhatia
- ICARE Eye Hospital & Postgraduate Institute, Noida, U.P., India
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28
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Kim S, Dorlhiac G, Cotrim Chaves R, Zalavadia M, Streets A. Paper-thin multilayer microfluidic devices with integrated valves. LAB ON A CHIP 2021; 21:1287-1298. [PMID: 33690757 DOI: 10.1039/d0lc01217c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Integrated valve microfluidics has an unparalleled capability to automate rapid delivery of fluids at the nanoliter scale for high-throughput biological experimentation. However, multilayer soft lithography, which is used to fabricate valve-microfluidics, produces devices with a minimum thickness of around five millimeters. This form-factor limitation prevents the use of such devices in experiments with limited sample thickness tolerance such as 4-pi microscopy, stimulated Raman scattering microscopy, and many forms of optical or magnetic tweezer applications. We present a new generation of integrated valve microfluidic devices that are less than 300 μm thick, including the cover-glass substrate, that resolves the thickness limitation. This "thin-chip" was fabricated through a novel soft-lithography technique that produces on-chip micro-valves with the same functionality and reliability of traditional thick valve-microfluidic devices despite the orders of magnitude reduction in thickness. We demonstrated the advantage of using our thin-chip over traditional thick devices to automate fluid control while imaging on a high-resolution inverted microscope. First, we demonstrate that the thin-chip provides an improved signal to noise when imaging single cells with two-color stimulated Raman scattering (SRS). We then demonstrated how the thin-chip can be used to simultaneously perform on-chip magnetic manipulation of beads and fluorescent imaging. This study reveals the potential of our thin-chip in high-resolution imaging, sorting, and bead capture-based single-cell multi-omics applications.
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Affiliation(s)
- Soohong Kim
- Ningbo University, College of Food and Pharmaceutical Sciences, Ningbo, Zhejiang 315832, China
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29
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Cahn JKB, Piel J. Opening up the Single-Cell Toolbox for Microbial Natural Products Research. Angew Chem Int Ed Engl 2021; 60:18412-18428. [PMID: 30748086 DOI: 10.1002/anie.201900532] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Indexed: 02/06/2023]
Abstract
The diverse microbes that produce natural products represent an important source of novel therapeutics, drug leads, and scientific tools. However, the vast majority have not been grown in axenic culture and are members of complex communities. While meta-'omic methods such as metagenomics, -transcriptomics, and -proteomics reveal collective molecular features of this "microbial dark matter", the study of individual microbiome members can be challenging. To address these limits, a number of techniques with single-bacterial resolution have been developed in the last decade and a half. While several of these are embraced by microbial ecologists, there has been less use by researchers interested in mining microbes for natural products. In this review, we discuss the available and emerging techniques for targeted single-cell analysis with a particular focus on applications to the discovery and study of natural products.
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Affiliation(s)
- Jackson K B Cahn
- Instit. of Microbiol., Eidgenössische Technische Hochschule Zürich (ETH), 8093, Zurich, Switzerland
| | - Jörn Piel
- Instit. of Microbiol., Eidgenössische Technische Hochschule Zürich (ETH), 8093, Zurich, Switzerland
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30
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Jurinjak Tušek A, Šalić A, Valinger D, Jurina T, Benković M, Kljusurić JG, Zelić B. The power of microsystem technology in the food industry – Going small makes it better. INNOV FOOD SCI EMERG 2021. [DOI: 10.1016/j.ifset.2021.102613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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31
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Huo W, Ling W, Wang Z, Li Y, Zhou M, Ren M, Li X, Li J, Xia Z, Liu X, Huang X. Miniaturized DNA Sequencers for Personal Use: Unreachable Dreams or Achievable Goals. FRONTIERS IN NANOTECHNOLOGY 2021. [DOI: 10.3389/fnano.2021.628861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The appearance of next generation sequencing technology that features short read length with high measurement throughput and low cost has revolutionized the field of life science, medicine, and even computer science. The subsequent development of the third-generation sequencing technologies represented by nanopore and zero-mode waveguide techniques offers even higher speed and long read length with promising applications in portable and rapid genomic tests in field. Especially under the current circumstances, issues such as public health emergencies and global pandemics impose soaring demand on quick identification of origins and species of analytes through DNA sequences. In addition, future development of disease diagnosis, treatment, and tracking techniques may also require frequent DNA testing. As a result, DNA sequencers with miniaturized size and highly integrated components for personal and portable use to tackle increasing needs for disease prevention, personal medicine, and biohazard protection may become future trends. Just like many other biological and medical analytical systems that were originally bulky in sizes, collaborative work from various subjects in engineering and science eventually leads to the miniaturization of these systems. DNA sequencers that involve nanoprobes, detectors, microfluidics, microelectronics, and circuits as well as complex functional materials and structures are extremely complicated but may be miniaturized with technical advancement. This paper reviews the state-of-the-art technology in developing essential components in DNA sequencers and analyzes the feasibility to achieve miniaturized DNA sequencers for personal use. Future perspectives on the opportunities and associated challenges for compact DNA sequencers are also identified.
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32
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Altemose N, Maslan A, Rios-Martinez C, Lai A, White JA, Streets A. μDamID: A Microfluidic Approach for Joint Imaging and Sequencing of Protein-DNA Interactions in Single Cells. Cell Syst 2020; 11:354-366.e9. [PMID: 33099405 PMCID: PMC7588622 DOI: 10.1016/j.cels.2020.08.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 07/01/2020] [Accepted: 08/22/2020] [Indexed: 12/23/2022]
Abstract
DNA adenine methyltransferase identification (DamID) measures a protein's DNA-binding history by methylating adenine bases near each protein-DNA interaction site and then selectively amplifying and sequencing these methylated regions. Additionally, these interactions can be visualized using m6A-Tracer, a fluorescent protein that binds to methyladenines. Here, we combine these imaging and sequencing technologies in an integrated microfluidic platform (μDamID) that enables single-cell isolation, imaging, and sorting, followed by DamID. We use μDamID and an improved m6A-Tracer protein to generate paired imaging and sequencing data from individual human cells. We validate interactions between Lamin-B1 protein and lamina-associated domains (LADs), observe variable 3D chromatin organization and broad gene regulation patterns, and jointly measure single-cell heterogeneity in Dam expression and background methylation. μDamID provides the unique ability to compare paired imaging and sequencing data for each cell and between cells, enabling the joint analysis of the nuclear localization, sequence identity, and variability of protein-DNA interactions. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
- Nicolas Altemose
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Annie Maslan
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Carolina Rios-Martinez
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andre Lai
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jonathan A White
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Aaron Streets
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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Tan HY, Toh YC. What can microfluidics do for human microbiome research? BIOMICROFLUIDICS 2020; 14:051303. [PMID: 33062112 PMCID: PMC7538166 DOI: 10.1063/5.0012185] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/17/2020] [Indexed: 05/13/2023]
Abstract
Dysregulation of the human microbiome has been linked to various disease states, which has galvanized the efforts to modulate human health through microbiomes. Currently, human microbiome research is going through several phases to identify the constituent components of the microbiome, associate microbiome changes with physiological and pathological states, understand causative relationships, and finally translate this knowledge into therapeutics and diagnostics. The convergence of microfluidic technologies with molecular and cell profiling, microbiology, and tissue engineering can potentially be applied to these different phases of microbiome research to overcome the existing challenges faced by conventional approaches. The goal of this paper is to discuss and highlight the opportunities of applying different microfluidic technologies to specific areas of microbiome research as well as unique challenges that microfluidics must overcome when working with microbiome-relevant biological materials, e.g., micro-organisms, host tissues, and fluids. We will discuss the applicability of integrated microfluidic systems for processing biological samples for genomic sequencing analyses. For functional analysis of the microbiota, we will cover state-of-the-art microfluidic devices for microbiota cultivation and functional measurements. Finally, we highlight the use of organs-on-chips to model various microbiome-host tissue interactions. We envision that microfluidic technologies may hold great promise in advancing the knowledge on the interplay between microbiome and human health, as well as its eventual translation into microbiome-based diagnostics and therapeutics.
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Affiliation(s)
- Hsih-Yin Tan
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599
| | - Yi-Chin Toh
- Author to whom correspondence should be addressed:
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Microbial single-cell omics: the crux of the matter. Appl Microbiol Biotechnol 2020; 104:8209-8220. [PMID: 32845367 PMCID: PMC7471194 DOI: 10.1007/s00253-020-10844-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/08/2020] [Accepted: 08/17/2020] [Indexed: 01/10/2023]
Abstract
Abstract Single-cell genomics and transcriptomics can provide reliable context for assembled genome fragments and gene expression activity on the level of individual prokaryotic genomes. These methods are rapidly emerging as an essential complement to cultivation-based, metagenomics, metatranscriptomics, and microbial community-focused research approaches by allowing direct access to information from individual microorganisms, even from deep-branching phylogenetic groups that currently lack cultured representatives. Their integration and binning with environmental ‘omics data already provides unprecedented insights into microbial diversity and metabolic potential, enabling us to provide information on individual organisms and the structure and dynamics of natural microbial populations in complex environments. This review highlights the pitfalls and recent advances in the field of single-cell omics and its importance in microbiological and biotechnological studies. Key points • Single-cell omics expands the tree of life through the discovery of novel organisms, genes, and metabolic pathways. • Disadvantages of metagenome-assembled genomes are overcome by single-cell omics. • Functional analysis of single cells explores the heterogeneity of gene expression. • Technical challenges still limit this field, thus prompting new method developments.
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35
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Hess JF, Kotrová M, Calabrese S, Darzentas N, Hutzenlaub T, Zengerle R, Brüggemann M, Paust N. Automation of Amplicon-Based Library Preparation for Next-Generation Sequencing by Centrifugal Microfluidics. Anal Chem 2020; 92:12833-12841. [DOI: 10.1021/acs.analchem.0c01202] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Jacob Friedrich Hess
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Michaela Kotrová
- Unit for Hematological Diagnostics, II. Medical Department, University Medical Center Schleswig Holstein, Langer Segen 8-10, 24105 Kiel, Germany
| | - Silvia Calabrese
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Nikos Darzentas
- Unit for Hematological Diagnostics, II. Medical Department, University Medical Center Schleswig Holstein, Langer Segen 8-10, 24105 Kiel, Germany
| | - Tobias Hutzenlaub
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Roland Zengerle
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Monika Brüggemann
- Unit for Hematological Diagnostics, II. Medical Department, University Medical Center Schleswig Holstein, Langer Segen 8-10, 24105 Kiel, Germany
| | - Nils Paust
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
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36
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Hess J, Kohl T, Kotrová M, Rönsch K, Paprotka T, Mohr V, Hutzenlaub T, Brüggemann M, Zengerle R, Niemann S, Paust N. Library preparation for next generation sequencing: A review of automation strategies. Biotechnol Adv 2020; 41:107537. [DOI: 10.1016/j.biotechadv.2020.107537] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/27/2020] [Accepted: 03/16/2020] [Indexed: 01/08/2023]
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37
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French S, Farha M, Ellis MJ, Sameer Z, Côté JP, Cotroneo N, Lister T, Rubio A, Brown ED. Potentiation of Antibiotics against Gram-Negative Bacteria by Polymyxin B Analogue SPR741 from Unique Perturbation of the Outer Membrane. ACS Infect Dis 2020; 6:1405-1412. [PMID: 31566948 DOI: 10.1021/acsinfecdis.9b00159] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Therapeutics targeting Gram-negative bacteria have the challenge of overcoming a formidable outer membrane (OM) barrier. Here, we characterize the action of SPR741, a novel polymyxin B (PMB) analogue shown to potentiate several large-scaffold antibiotics in Gram-negative pathogens. Probing the surface topology of Escherichia coli using atomic force microscopy revealed substantial OM disorder at concentrations of SPR741 that lead to antibiotic potentiation. Conversely, very little cytoplasmic membrane depolarization was observed at these same concentrations, indicating that SPR741 acts predominately on the OM. Truncating the lipopolysaccharide (LPS) core with genetic perturbations uniquely sensitized E. coli to SPR741, suggesting that LPS core residues keep SPR741 at the OM, where it can potentiate a codrug, rather than permit its entry to the cytoplasmic membrane. Further, a promoter activity assay revealed that SPR741 challenge induced the expression of RcsAB, a stress sensor for OM perturbation. Together, these results indicate that SPR741 interacts predominately with the OM, in contrast to the dual action of PMB and colistin at both the outer and cytoplasmic membranes.
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Affiliation(s)
- Shawn French
- Department of Biochemistry and Biomedical Science and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Maya Farha
- Department of Biochemistry and Biomedical Science and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Michael J. Ellis
- Department of Biochemistry and Biomedical Science and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Zaid Sameer
- Department of Biochemistry and Biomedical Science and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Jean-Philippe Côté
- Department of Biochemistry and Biomedical Science and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Nicole Cotroneo
- Spero Therapeutics, 675 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Troy Lister
- Spero Therapeutics, 675 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Aileen Rubio
- Spero Therapeutics, 675 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Eric D. Brown
- Department of Biochemistry and Biomedical Science and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
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Continuous Microfluidic Purification of DNA Using Magnetophoresis. MICROMACHINES 2020; 11:mi11020187. [PMID: 32054004 PMCID: PMC7074667 DOI: 10.3390/mi11020187] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/13/2022]
Abstract
Automatic microfluidic purification of nucleic acid is predictable to reduce the input of original samples and improve the throughput of library preparation for sequencing. Here, we propose a novel microfluidic system using an external NdFeB magnet to isolate DNA from the polymerase chain reaction (PCR) mixture. The DNA was purified and isolated when the DNA-carrying beads transported to the interface of multi-laminar flow under the influence of magnetic field. Prior to the DNA recovery experiments, COMSOL simulations were carried out to study the relationship between trajectory of beads and magnet positions as well as fluid velocities. Afterwards, the experiments to study the influence of varying velocities and input of samples on the DNA recovery were conducted. Compared to experimental results, the relative error of the final position of beads is less than 10%. The recovery efficiency decreases with increase of input or fluid velocity, and the maximum DNA recovery efficiency is 98.4% with input of l00 ng DNA at fluid velocity of 1.373 mm/s. The results show that simulations significantly reduce the time for parameter adjustment in experiments. In addition, this platform uses a basic two-layer chip to realize automatic DNA isolation without any other liquid switch value or magnet controller.
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Murphy TW, Hsieh YP, Zhu B, Naler LB, Lu C. Microfluidic Platform for Next-Generation Sequencing Library Preparation with Low-Input Samples. Anal Chem 2020; 92:2519-2526. [PMID: 31894965 PMCID: PMC7002211 DOI: 10.1021/acs.analchem.9b04086] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Advances in next-generation sequencing (NGS) have made available a wealth of information that had previously been inaccessible to researchers and clinicians. NGS has been applied to understand genomic, transcriptomic, and epigenomic changes and gained traction as a significant tool capable of accelerating diagnosis, prognosis, and biomarker discovery. However, these NGS assays have yet to be practical methods for patient stratification or diagnosis because of the gap between the tiny quantities of biomaterials provided by a clinical sample and the large DNA input required by most of these assays. Current library preparation methodologies typically require large input amounts of DNA and a long and complicated manual process. Here, we present a microfluidic droplet-based system for NGS library preparation, capable of reducing the number of pipetting steps significantly, reducing reagent consumption by 10×, and automating much of the process, while supporting an extremely low DNA input requirement (10 pg per library). This semiautomated technology will allow for low-input preparations of 8 libraries simultaneously while reducing batch-to-batch variation and operator hands-on time.
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Affiliation(s)
- Travis W. Murphy
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061
| | - Yuan-Pang Hsieh
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061
| | - Bohan Zhu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061
| | - Lynette B. Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061
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40
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Palace SG, Wang Y, Rubin DHF, Welsh MA, Mortimer TD, Cole K, Eyre DW, Walker S, Grad YH. RNA polymerase mutations cause cephalosporin resistance in clinical Neisseria gonorrhoeae isolates. eLife 2020; 9:e51407. [PMID: 32011233 PMCID: PMC7012608 DOI: 10.7554/elife.51407] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 02/01/2020] [Indexed: 02/06/2023] Open
Abstract
Increasing Neisseria gonorrhoeae resistance to ceftriaxone, the last antibiotic recommended for empiric gonorrhea treatment, poses an urgent public health threat. However, the genetic basis of reduced susceptibility to ceftriaxone is not completely understood: while most ceftriaxone resistance in clinical isolates is caused by target site mutations in penA, some isolates lack these mutations. We show that penA-independent ceftriaxone resistance has evolved multiple times through distinct mutations in rpoB and rpoD. We identify five mutations in these genes that each increase resistance to ceftriaxone, including one mutation that arose independently in two lineages, and show that clinical isolates from multiple lineages are a single nucleotide change from ceftriaxone resistance. These RNA polymerase mutations cause large-scale transcriptional changes without altering susceptibility to other antibiotics, reducing growth rate, or deranging cell morphology. These results underscore the unexpected diversity of pathways to resistance and the importance of continued surveillance for novel resistance mutations.
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Affiliation(s)
- Samantha G Palace
- Department of Immunology and Infectious DiseasesHarvard T. H. Chan School of Public HealthBostonUnited States
- Center for Communicable Disease DynamicsHarvard T. H. Chan School of Public HealthBostonUnited States
| | - Yi Wang
- Department of Immunology and Infectious DiseasesHarvard T. H. Chan School of Public HealthBostonUnited States
| | - Daniel HF Rubin
- Department of Immunology and Infectious DiseasesHarvard T. H. Chan School of Public HealthBostonUnited States
| | - Michael A Welsh
- Department of MicrobiologyHarvard Medical SchoolBostonUnited States
| | - Tatum D Mortimer
- Department of Immunology and Infectious DiseasesHarvard T. H. Chan School of Public HealthBostonUnited States
| | - Kevin Cole
- Public Health England, Royal Sussex County HospitalBrightonUnited Kingdom
| | - David W Eyre
- Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Suzanne Walker
- Department of MicrobiologyHarvard Medical SchoolBostonUnited States
| | - Yonatan H Grad
- Department of Immunology and Infectious DiseasesHarvard T. H. Chan School of Public HealthBostonUnited States
- Center for Communicable Disease DynamicsHarvard T. H. Chan School of Public HealthBostonUnited States
- Division of Infectious DiseasesBrigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
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Xia Y, Chen Y, Tang Y, Cheng G, Yu X, He H, Cao G, Lu H, Liu Z, Zheng SY. Smartphone-Based Point-of-Care Microfluidic Platform Fabricated with a ZnO Nanorod Template for Colorimetric Virus Detection. ACS Sens 2019; 4:3298-3307. [PMID: 31769284 DOI: 10.1021/acssensors.9b01927] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Viruses pose serious infectious disease threats to humans and animals. To significantly decrease the mortality and morbidity caused by virus infections, there is an urgent need of sensitive and rapid point-of-care platforms for virus detection, especially in low-resource settings. Herein, we developed a smartphone-based point-of-care platform for highly sensitive and selective detection of the avian influenza virus based on nanomaterial-enabled colorimetric detection. The 3D nanostructures, which serve as a scaffold for antibody conjugation to capture the avian influenza virus, are made on PDMS herringbone structures with a ZnO nanorod template. After virus capture, the on-chip gold nanoparticle-based colorimetric reaction allows virus detection by naked eyes with a detection limit of 2.7 × 104 EID50/mL, which is one order of magnitude better than that of conventional fluorescence-based ELISA. Furthermore, a smartphone imaging system with data processing capability further improves the detection limit, reaching down to 8 × 103 EID50/mL. The entire virus capture and detection process can be completed in 1.5 h. We envision that this point-of-care microfluidic system integrated with smartphone imaging and colorimetric detection would provide a fast, cheap, sensitive, and user-friendly platform for virus detection in low-resource settings.
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42
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Droplet-based optofluidic systems for measuring enzyme kinetics. Anal Bioanal Chem 2019; 412:3265-3283. [PMID: 31853606 DOI: 10.1007/s00216-019-02294-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/15/2019] [Accepted: 11/19/2019] [Indexed: 01/05/2023]
Abstract
The study of enzyme kinetics is of high significance in understanding metabolic networks in living cells and using enzymes in industrial applications. To gain insight into the catalytic mechanisms of enzymes, it is necessary to screen an enormous number of reaction conditions, a process that is typically laborious, time-consuming, and costly when using conventional measurement techniques. In recent times, droplet-based microfluidic systems have proved themselves to be of great utility in large-scale biological experimentation, since they consume a minimal sample, operate at high analytical throughput, are characterized by efficient mass and heat transfer, and offer high levels of integration and automation. The primary goal of this review is the introduction of novel microfluidic tools and detection methods for use in high-throughput and sensitive analysis of enzyme kinetics. The first part of this review focuses on introducing basic concepts of enzyme kinetics and describing most common microfluidic approaches, with a particular focus on segmented flow. Herein, the key advantages include accurate control over the flow behavior, efficient mass and heat transfer, multiplexing, and high-level integration with detection modalities. The second part describes the current state-of-the-art platforms for high-throughput and sensitive analysis of enzyme kinetics. In addition to our categorization of recent advances in measuring enzyme kinetics, we have endeavored to critically assess the limitations of each of these detection approaches and propose strategies to improve measurements in droplet-based microfluidics. Graphical abstract.
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43
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Xia L, Yang J, Su R, Zhou W, Zhang Y, Zhong Y, Huang S, Chen Y, Li G. Recent Progress in Fast Sample Preparation Techniques. Anal Chem 2019; 92:34-48. [DOI: 10.1021/acs.analchem.9b04735] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ling Xia
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
| | - Jiani Yang
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
| | - Rihui Su
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
| | - Wanjun Zhou
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
| | - Yanshu Zhang
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
| | - Yanhui Zhong
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
| | - Simin Huang
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
| | - Yanlong Chen
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
| | - Gongke Li
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
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44
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Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R. Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads. Genome Biol 2019; 20:226. [PMID: 31672156 PMCID: PMC6822431 DOI: 10.1186/s13059-019-1834-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 09/23/2019] [Indexed: 01/05/2023] Open
Abstract
As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach leaderboard metagenome sequencing. To explore protocol optimization for leaderboard metagenomics in real samples, we introduce a benchmark of library prep and sequencing using internal references generated by synthetic long-read technology, allowing us to evaluate high-throughput library preparation methods against gold-standard reference genomes derived from the samples themselves. We introduce a low-cost protocol for high-throughput library preparation and sequencing.
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Affiliation(s)
- Jon G Sanders
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Sergey Nurk
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Rodolfo A Salido
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Jeremiah Minich
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Zhenjiang Z Xu
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Marcus Fedarko
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Timothy D Arthur
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | | | - Brigid S Boland
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA, USA
| | - Greg C Humphrey
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Caitriona Brennan
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Karenina Sanders
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - James Gaffney
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Mahdieh Khosroheidari
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Cliff Green
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Marlon Liyanage
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Jason W Dang
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Vanessa V Phelan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, CO, USA
| | - Robert A Quinn
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Anton Bankevich
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - John T Chang
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA, USA
| | - Tariq M Rana
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Douglas J Conrad
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - William J Sandborn
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Larry Smarr
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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45
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Cui X, Zhang H, Du H. Carbapenemases in Enterobacteriaceae: Detection and Antimicrobial Therapy. Front Microbiol 2019; 10:1823. [PMID: 31481937 PMCID: PMC6710837 DOI: 10.3389/fmicb.2019.01823] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) have spread rapidly around the world in the past few years, posing great challenges to human health. The plasmid-mediated horizontal transmission of carbapenem-resistance genes is the main cause of the surge in the prevalence of CRE. Therefore, the timely and accurate detection of CRE, especially carbapenemase-producing Enterobacteriaceae, is very important for the clinical prevention and treatment of these infections. A variety of methods for the rapid detection of CRE phenotypes and genotypes have been developed for use in clinical microbiology laboratories. To overcome the lack of efficient antibiotics, CRE infections are often treated with combination therapies. Moreover, novel drugs and emerging strategies appeared successively and in various stages of development. In this article, we summarized the global distribution of various carbapenemases. And we focused on summarizing and comparing the advantages and limitations of the detection methods and the therapeutic strategies of CRE primarily.
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Affiliation(s)
- Xiaoyan Cui
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Haifang Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
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46
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Gorgannezhad L, Stratton H, Nguyen NT. Microfluidic-Based Nucleic Acid Amplification Systems in Microbiology. MICROMACHINES 2019; 10:E408. [PMID: 31248141 PMCID: PMC6630468 DOI: 10.3390/mi10060408] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 02/07/2023]
Abstract
Rapid, sensitive, and selective bacterial detection is a hot topic, because the progress in this research area has had a broad range of applications. Novel and innovative strategies for detection and identification of bacterial nucleic acids are important for practical applications. Microfluidics is an emerging technology that only requires small amounts of liquid samples. Microfluidic devices allow for rapid advances in microbiology, enabling access to methods of amplifying nucleic acid molecules and overcoming difficulties faced by conventional. In this review, we summarize the recent progress in microfluidics-based polymerase chain reaction devices for the detection of nucleic acid biomarkers. The paper also discusses the recent development of isothermal nucleic acid amplification and droplet-based microfluidics devices. We discuss recent microfluidic techniques for sample preparation prior to the amplification process.
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Affiliation(s)
- Lena Gorgannezhad
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
- School of Environment and Science, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
| | - Helen Stratton
- School of Environment and Science, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
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47
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Li R, Gai W, Zhu D, Lok C, Song C, Dong J, Han N, Zhang Y, Zhao X. Evaluation of a novel micro/nanofluidic chip platform for the detection of influenza A and B virus in patients with influenza-like illness. AMB Express 2019; 9:77. [PMID: 31139958 PMCID: PMC6538719 DOI: 10.1186/s13568-019-0791-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 05/06/2019] [Indexed: 01/23/2023] Open
Abstract
We introduced a novel micro/nanofluidic chip platform (MNCP), which is based on an isothermal nucleic acid amplification method. This study aimed to evaluate the MNCP method for influenza A and B viruses detecting and subtyping using throat swab samples from patients with influenza-like illness (ILI). A total of 266 throat swab samples from 266 non-repeated patients with ILI were tested for influenza A and B viruses using three methods, MNCP, a rapid influenza diagnostic test (RIDT), and real-time reverse transcription polymerase chain reaction (rRT-PCR). The results of MNCP were compared to those obtained by rRT-PCR and RIDT and the performance of MNCP was further evaluated. Compared with rRT-PCR results, the rates of sensitivity, specificity, overall concordance, and the kappa value of MNCP were 98.89%, 96.97%, 97.65%, and 0.95 for influenza A virus; 94.95%, 99.38%, 97.68%, and 0.95 for influenza B virus, respectively. Subtypes of influenza A viruses, e.g., A(H1N1)pdm09, A(H3N2), and A(not subtyped), and influenza B viruses could be distinguished in one MNCP assay within 1 h. Compared with rRT-PCR and MNCP, RIDT showed poor clinical sensitivity for influenza virus detection. This study showed MNCP is rapid, sensitive and versatile detecting system with potential for clinical application in pathogen diagnosis for patients with ILI.
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Moreno-Molina M, Comas I, Furió V. The Future of TB Resistance Diagnosis: The Essentials on Whole Genome Sequencing and Rapid Testing Methods. Arch Bronconeumol 2019; 55:421-426. [PMID: 30795867 DOI: 10.1016/j.arbres.2019.01.002] [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: 10/16/2018] [Revised: 01/11/2019] [Accepted: 01/14/2019] [Indexed: 12/25/2022]
Abstract
Tuberculosis resistance diagnostics have vastly improved in recent years thanks to the development of standardised phenotypic and molecular testing methods. However, these methods are either slow or limited in the number of resistant genotypes they can detect. With the advent of next-generation sequencing (NGS) we can sidestep all those problems, as we can sequence whole tuberculosis genomes at increasingly smaller costs and requiring less and less DNA. In this review, we explain how accumulated knowledge in the field has allowed us to go from phenotypic testing to molecular methods to Whole Genome Sequencing (WGS) for resistance diagnostics. We compare current diagnostic methods with WGS as to their efficacy in detecting resistant cases, and show how forthcoming advances in NGS technologies will be crucial in widespread implementation of WGS as a diagnostic tool.
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Affiliation(s)
| | - Iñaki Comas
- Biomedicine Institute of Valencia (CSIC), Valencia, Spain; CIBER in Epidemiology and Public Health, Spain
| | - Victoria Furió
- Biomedicine Institute of Valencia (CSIC), Valencia, Spain.
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49
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Scheler O, Postek W, Garstecki P. Recent developments of microfluidics as a tool for biotechnology and microbiology. Curr Opin Biotechnol 2019; 55:60-67. [DOI: 10.1016/j.copbio.2018.08.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/13/2018] [Accepted: 08/09/2018] [Indexed: 02/07/2023]
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50
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Reyes M, Vickers D, Billman K, Eisenhaure T, Hoover P, Browne EP, Rao DA, Hacohen N, Blainey PC. Multiplexed enrichment and genomic profiling of peripheral blood cells reveal subset-specific immune signatures. SCIENCE ADVANCES 2019; 5:eaau9223. [PMID: 30746468 PMCID: PMC6357748 DOI: 10.1126/sciadv.aau9223] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/07/2018] [Indexed: 05/12/2023]
Abstract
Specialized immune cell subsets are involved in autoimmune disease, cancer immunity, and infectious disease through a diverse range of functions mediated by overlapping pathways and signals. However, subset-specific responses may not be detectable in analyses of whole blood samples, and no efficient approach for profiling cell subsets at high throughput from small samples is available. We present a low-input microfluidic system for sorting immune cells into subsets and profiling their gene expression. We validate the system's technical performance against standard subset isolation and library construction protocols and demonstrate the importance of subset-specific profiling through in vitro stimulation experiments. We show the ability of this integrated platform to identify subset-specific disease signatures by profiling four immune cell subsets in blood from patients with systemic lupus erythematosus (SLE) and matched control subjects. The platform has the potential to make multiplexed subset-specific analysis routine in many research laboratories and clinical settings.
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Affiliation(s)
- Miguel Reyes
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dwayne Vickers
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Paul Hoover
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Immunology, Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Deepak A. Rao
- Division of Rheumatology, Immunology, Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Corresponding author. (N.H.); (P.C.B.)
| | - Paul C. Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Corresponding author. (N.H.); (P.C.B.)
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