1
|
Zhang J, Huang Y, Bai N, Sun Y, Li K, Ruan H, Yan B, Hu J, Zhang N, Zhang H, Chen W, Fan D. Spirulina platensis components mitigate bone density loss induced by simulated microgravity: A mechanistic insight. Food Chem 2024; 463:141361. [PMID: 39340915 DOI: 10.1016/j.foodchem.2024.141361] [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: 06/13/2024] [Revised: 09/14/2024] [Accepted: 09/17/2024] [Indexed: 09/30/2024]
Abstract
In microgravity conditions, the consumption of Spirulina platensis (SP) as a renewable food source shows promise in mitigating osteoporosis due to its high nutritional content photosynthetic efficiency, environmental adaptability and positive effects on bone density, though the exact bioactive components and mechanisms remain unclear. Using a hindlimb suspension (HLS) model, this study investigated SP components: proteins (SPP), polysaccharides (SPS), lipids (SPL), and residue (SPR) on bone density and metabolism. Findings revealed that SPP and SPS significantly enhanced bone density and reduced oxidative stress. Activation of the FoxO3/Wnt/β-catenin pathway reduced FoxO3a expression and increased Wnt signaling molecules and β-catenin protein, boosting bone formation. Moreover, these components promoted beneficial gut bacteria like Turicibacter, reduced the Firmicutes-to-Bacteroidetes ratio, and enhanced SCFAs production, crucial for bone health. This study emphasized the potential of Spirulina nutrients in addressing space-induced osteoporosis and developing functional foods for long-term space missions.
Collapse
Affiliation(s)
- Jian Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yaxin Huang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Ning Bai
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Department of Endocrinology, Affiliated Hospital of Jiangnan University, Wuxi 214062, Jiangsu Province, China
| | - Yuying Sun
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Ke Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Huan Ruan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Bowen Yan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jian Hu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Chinese Cuisine Intangible Cultural Heritage Technology Inheritance, Ministry of Culture and Tourism, College of Tourism and Culinary Science, Yangzhou University, Yangzhou 225127, China
| | - Nana Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Daming Fan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Hess JF, Kotrová M, Fricke B, Songia S, Rigamonti S, Cavagna R, Tosi M, Paust N, Langerak AW, Spinelli O, Cazzaniga G, Brüggemann M, Hutzenlaub T. Clinical pilot study on microfluidic automation of IGH-VJ library preparation for next generation sequencing. Clin Chem Lab Med 2024; 62:e164-e167. [PMID: 38153095 DOI: 10.1515/cclm-2023-1346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/18/2023] [Indexed: 12/29/2023]
Affiliation(s)
- Jacob F Hess
- Hahn-Schickard, Freiburg, Germany
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Michaela Kotrová
- Unit for Hematological Diagnostics, II. Medical Department, University Medical Center Schleswig Holstein, Kiel, Germany
| | - Birgit Fricke
- Unit for Hematological Diagnostics, II. Medical Department, University Medical Center Schleswig Holstein, Kiel, Germany
| | - Simona Songia
- Centro Tettamanti, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Silvia Rigamonti
- Centro Tettamanti, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Roberta Cavagna
- Struttura Complessa Ematologia, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Manuela Tosi
- Struttura Complessa Ematologia, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Nils Paust
- Hahn-Schickard, Freiburg, Germany
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Anton W Langerak
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Orietta Spinelli
- Struttura Complessa Ematologia, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Giovanni Cazzaniga
- Centro Tettamanti, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- School of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Monika Brüggemann
- Unit for Hematological Diagnostics, II. Medical Department, University Medical Center Schleswig Holstein, Kiel, Germany
| | - Tobias Hutzenlaub
- Hahn-Schickard, Freiburg, Germany
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| |
Collapse
|
4
|
Ott O, Tolppi S, Figueroa-Cruz J, Myagmar K, Unurbuyan K, Tripathi A. Leveraging the fundamentals of heat transfer and fluid mechanics in microscale geometries for automated next-generation sequencing library preparation. Sci Rep 2024; 14:12564. [PMID: 38822053 DOI: 10.1038/s41598-024-63014-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/23/2024] [Indexed: 06/02/2024] Open
Abstract
Next-generation sequencing (NGS) is emerging as a powerful tool for molecular diagnostics but remains limited by cumbersome and inefficient sample preparation. We present an innovative automated NGS library preparation system with a simplified mechanical design that exploits both macro- and microfluidic properties for optimizing heat transfer, reaction kinetics, mass transfer, fluid mechanics, adsorption-desorption rates, and molecular thermodynamics. Our approach introduces a unique two-cannula cylindrical capillary system connected to a programmable syringe pump and a Peltier heating element able to execute all steps with high efficiency. Automatic reagent movement, mixing, and magnetic bead-based washing with capillary-based thermal cycling (capillary-PCR) are completely integrated into a single platform. The manual 3-h library preparation process is reduced to less than 15 min of hands-on time via optimally pre-plated reagent plates, followed by less than 6 h of instrument run time during which no user interaction is required. We applied this method to two library preparation assays with different DNA fragmentation requirements (mechanical vs. enzymatic fragmentation), sufficiently limiting consumable use to one cartridge and one 384 well-plate per run. Our platform successfully prepared eight libraries in parallel, generating sequencing data for both human and Escherichia coli DNA libraries with negligible coverage bias compared to positive controls. All sequencing data from our libraries attained Phred (Q) scores > 30, mapping to reference genomes at 99% confidence. The method achieved final library concentrations and size distributions comparable with the conventional manual approach, demonstrating compatibility with downstream sequencing and subsequent data analysis. Our engineering design offers repeatability and consistency in the quality of sequence-able libraries, asserting the importance of mechanical design considerations that employ and optimize fundamental fluid mechanics and heat transfer properties. Furthermore in this work, we provide unique insights into the mechanisms of sample loss within NGS library preparation assays compared with automated adaptations and pinpoint areas in which the principles of thermodynamics, fluid mechanics, and heat transfer can improve future mechanical design iterations.
Collapse
Affiliation(s)
- Olivia Ott
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Sabrina Tolppi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Jennifer Figueroa-Cruz
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Khaliun Myagmar
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Khulan Unurbuyan
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA.
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Li S, Wan C, Wang B, Chen D, Zeng W, Hong X, Li L, Pang Z, Du W, Feng X, Chen P, Li Y, Liu BF. Handyfuge Microfluidic for On-Site Antibiotic Susceptibility Testing. Anal Chem 2023; 95:6145-6155. [PMID: 36996249 DOI: 10.1021/acs.analchem.3c00557] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Low-cost, rapid, and accurate acquisition of minimum inhibitory concentrations (MICs) is key to limiting the development of antimicrobial resistance (AMR). Until now, conventional antibiotic susceptibility testing (AST) methods are typically time-consuming, high-cost, and labor-intensive, making them difficult to accomplish this task. Herein, an electricity-free, portable, and robust handyfuge microfluidic chip was developed for on-site AST, termed handyfuge-AST. With simply handheld centrifugation, the bacterial-antibiotic mixtures with accurate antibiotic concentration gradients could be generated in less than 5 min. The accurate MIC values of single antibiotics (including ampicillin, kanamycin, and chloramphenicol) or their combinations against Escherichia coli could be obtained within 5 h. To further meet the growing demands of point-of-care testing, we upgraded our handyfuge-AST with a pH-based colorimetric strategy, enabling naked eye recognition or intelligent recognition with a homemade mobile app. Through a comparative study of 60 clinical data (10 clinical samples corresponding to six commonly used antibiotics), the accurate MICs by handyfuge-AST with 100% categorical agreements were achieved compared to clinical standard methods (area under curves, AUCs = 1.00). The handyfuge-AST could be used as a low-cost, portable, and robust point-of-care device to rapidly obtain accurate MIC values, which significantly limit the progress of AMR.
Collapse
Affiliation(s)
- Shunji Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Chao Wan
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Bangfeng Wang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Dongjuan Chen
- Department of Laboratory Medicine, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430070, China
| | - Wenyi Zeng
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xianzhe Hong
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Lina Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zheng Pang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Wei Du
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaojun Feng
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Peng Chen
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yiwei Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| |
Collapse
|
7
|
Schlenker F, Juelg P, Lüddecke J, Paust N, Zengerle R, Hutzenlaub T. Nanobead handling on a centrifugal microfluidic LabDisk for automated extraction of cell-free circulating DNA with high recovery rates. Analyst 2023; 148:932-941. [PMID: 36722841 DOI: 10.1039/d2an01820a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
cfDNA is an emerging biomarker with promising uses for the monitoring of cancer or infectious disease diagnostics. This work demonstrates a new concept for an automated cfDNA extraction with nanobeads as the solid phase in a centrifugal microfluidic LabDisk. By using a combination of centrifugal and magnetic forces, we retain the nanobeads in one incubation chamber while sequentially adding, incubating and removing the sample and pre-stored buffers for extraction. As the recovery rate of the typically low concentration of cfDNA is of high importance to attain sufficient amounts for analysis, optimal beadhandling is paramount. The goal is that the cfDNA in the sample adsorbs to the solid phase completely during the binding step, is retained during washing and completely removed during elution. In this work, we improved beadhandling by optimizing the incubation chamber geometry and both frequency and temperature protocols, to maximize recovery rates. For characterization of the extraction performance, synthetic mutant DNA was spiked into human plasma samples. The LabDisk showed better reproducibility in DNA recovery rates with a standard deviation of ±13% compared to a manual approach using spin-columns (±17%) or nanobeads (±26%). The extraction of colorectal cancer samples with both the developed LabDisk and a robotic automation instrument resulted in comparable allele frequencies. Consequently, we present a highly attractive solution for an automated liquid biopsy cfDNA extraction in a small benchtop device.
Collapse
Affiliation(s)
| | - Peter Juelg
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany. .,Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Jan Lüddecke
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany. .,Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Nils Paust
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany. .,Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Roland Zengerle
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany. .,Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Tobias Hutzenlaub
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany. .,Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| |
Collapse
|