1
|
Philpott DN, Chen K, Atwal RS, Li D, Christie J, Sargent EH, Kelley SO. Ultrathroughput immunomagnetic cell sorting platform. LAB ON A CHIP 2022; 22:4822-4830. [PMID: 36382608 DOI: 10.1039/d2lc00798c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
High-throughput phenotypic cell sorting is critical to the development of cell-based therapies and cell screening discovery platforms. However, current cytometry platforms are limited by throughput, number of fractionated populations that can be isolated, cell viability, and cost. We present an ultrathroughput microfluidic cell sorter capable of processing hundreds of millions of live cells per hour per device based on protein expression. This device, a next-generation microfluidic cell sorter (NG-MICS), combines multiple technologies, including 3D printing, reversible clamp sealing, and superhydrophobic treatments to create a reusable and user-friendly platform ready for deployment. The utility of such a platform is demonstrated through the rapid isolation of mature natural killer cells from peripheral blood mononuclear cells, for use in CAR-NK therapies at clinically-relevant scale.
Collapse
Affiliation(s)
- David N Philpott
- Edward S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Kangfu Chen
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Randy S Atwal
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA.
| | - Derek Li
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Jessie Christie
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Edward H Sargent
- Edward S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Electrical and Computer Engineering, Northwestern University, Evanston, IL, USA
| | - Shana O Kelley
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA.
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Chemistry, Northwestern University, Evanston, IL, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| |
Collapse
|
2
|
Kärcher J, Schulze B, Dörr A, Tierling S, Walter J. Transfer of blocker-based qPCR reactions for DNA methylation analysis into a microfluidic LoC system using thermal modeling. BIOMICROFLUIDICS 2022; 16:064102. [PMID: 36506005 PMCID: PMC9729016 DOI: 10.1063/5.0108374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
Changes in the DNA methylation landscape are associated with many diseases like cancer. Therefore, DNA methylation analysis is of great interest for molecular diagnostics and can be applied, e.g., for minimally invasive diagnostics in liquid biopsy samples like blood plasma. Sensitive detection of local de novo methylation, which occurs in various cancer types, can be achieved with quantitative HeavyMethyl-PCR using oligonucleotides that block the amplification of unmethylated DNA. A transfer of these quantitative PCRs (qPCRs) into point-of-care (PoC) devices like microfluidic Lab-on-Chip (LoC) cartridges can be challenging as LoC systems show significantly different thermal properties than qPCR cyclers. We demonstrate how an adequate thermal model of the specific LoC system can help us to identify a suitable thermal profile, even for complex HeavyMethyl qPCRs, with reduced experimental effort. Using a simulation-based approach, we demonstrate a proof-of-principle for the successful LoC transfer of colorectal SEPT9/ACTB-qPCR from Epi Procolon® colorectal carcinoma test, by avoidance of oligonucleotide interactions.
Collapse
Affiliation(s)
- Janik Kärcher
- Robert Bosch GmbH, Corporate Research, Robert Bosch Campus 1, 71272 Renninge, Germany
| | - Britta Schulze
- Robert Bosch GmbH, Corporate Research, Robert Bosch Campus 1, 71272 Renninge, Germany
| | - Aaron Dörr
- Robert Bosch GmbH, Corporate Research, Robert Bosch Campus 1, 71272 Renninge, Germany
| | - Sascha Tierling
- University of Saarland, Institute for Genetics and Epigenetics, Campus Saarbrücken, 66123 Saarbrücken, Germany
| | - Jörn Walter
- University of Saarland, Institute for Genetics and Epigenetics, Campus Saarbrücken, 66123 Saarbrücken, Germany
| |
Collapse
|
3
|
Kerk YJ, Jameel A, Xing X, Zhang C. Recent advances of integrated microfluidic suspension cell culture system. ENGINEERING BIOLOGY 2021; 5:103-119. [PMID: 36970555 PMCID: PMC9996741 DOI: 10.1049/enb2.12015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/19/2022] Open
Abstract
Microfluidic devices with superior microscale fluid manipulation ability and large integration flexibility offer great advantages of high throughput, parallelisation and multifunctional automation. Such features have been extensively utilised to facilitate cell culture processes such as cell capturing and culturing under controllable and monitored conditions for cell-based assays. Incorporating functional components and microfabricated configurations offered different levels of fluid control and cell manipulation strategies to meet diverse culture demands. This review will discuss the advances of single-phase flow and droplet-based integrated microfluidic suspension cell culture systems and their applications for accelerated bioprocess development, high-throughput cell selection, drug screening and scientific research to insight cell biology. Challenges and future prospects for this dynamically developing field are also highlighted.
Collapse
Affiliation(s)
- Yi Jing Kerk
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
| | - Aysha Jameel
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- MOE Key Laboratory of Industrial BiocatalysisDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
| | - Xin‐Hui Xing
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- MOE Key Laboratory of Industrial BiocatalysisDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- Center for Synthetic and Systems BiologyTsinghua UniversityBeijingChina
| | - Chong Zhang
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- MOE Key Laboratory of Industrial BiocatalysisDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- Center for Synthetic and Systems BiologyTsinghua UniversityBeijingChina
| |
Collapse
|
4
|
Chai H, Feng Y, Liang F, Wang W. A microfluidic device enabling deterministic single cell trapping and release. LAB ON A CHIP 2021; 21:2486-2494. [PMID: 34047733 DOI: 10.1039/d1lc00302j] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Successful single-cell isolation is a pivotal technique for subsequent biological and chemical analysis of single cells. Although significant advances have been made in single-cell isolation and analysis techniques, most passive microfluidic devices cannot deterministically release trapped cells for further analysis. In this paper, we present a novel microfluidic device that can achieve high-efficiency cell trapping, which can then be released in a deterministic order. The device contains an array of trapping sites, a main channel, a trigger channel, and an air channel. Two types of capillary valves are configured along the channels. As these capillary valves can be automatically opened in a predefined pattern, the incoming cells can be spontaneously and sequentially trapped into separate trapping sites. After trapping, the individual trapped cells can be released from their sites in a last-trapped-first-released manner by applying pressure from the trigger channel to counteract against the pressure from the main channel. The theoretical model of the trapping and release flow field is established respectively to describe the conditions required for trapping and release. Experiments using MCF-7 cells demonstrated the capability of our device for deterministic single cell trapping and release. We envision that our method constitutes a useful sample preparation platform for single cell analysis.
Collapse
Affiliation(s)
- Huichao Chai
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, China.
| | - Yongxiang Feng
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, China.
| | - Fei Liang
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, China.
| | - Wenhui Wang
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, China.
| |
Collapse
|
5
|
Shin H, Seo D, Choi Y. Extracellular Vesicle Identification Using Label-Free Surface-Enhanced Raman Spectroscopy: Detection and Signal Analysis Strategies. Molecules 2020; 25:E5209. [PMID: 33182340 PMCID: PMC7664897 DOI: 10.3390/molecules25215209] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/19/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EVs) have been widely investigated as promising biomarkers for the liquid biopsy of diseases, owing to their countless roles in biological systems. Furthermore, with the notable progress of exosome research, the use of label-free surface-enhanced Raman spectroscopy (SERS) to identify and distinguish disease-related EVs has emerged. Even in the absence of specific markers for disease-related EVs, label-free SERS enables the identification of unique patterns of disease-related EVs through their molecular fingerprints. In this review, we describe label-free SERS approaches for disease-related EV pattern identification in terms of substrate design and signal analysis strategies. We first describe the general characteristics of EVs and their SERS signals. We then present recent works on applied plasmonic nanostructures to sensitively detect EVs and notable methods to interpret complex spectral data. This review also discusses current challenges and future prospects of label-free SERS-based disease-related EV pattern identification.
Collapse
Affiliation(s)
- Hyunku Shin
- Department of Bio-convergence Engineering, Korea University, Seoul 02841, Korea; (H.S.); (D.S.)
| | - Dongkwon Seo
- Department of Bio-convergence Engineering, Korea University, Seoul 02841, Korea; (H.S.); (D.S.)
| | - Yeonho Choi
- Department of Bio-convergence Engineering, Korea University, Seoul 02841, Korea; (H.S.); (D.S.)
- School of Biomedical Engineering, Korea University, Seoul 02841, Korea
| |
Collapse
|
6
|
Zhuang J, Huo Q, Yang F, Xie N. Perspectives on the Role of Histone Modification in Breast Cancer Progression and the Advanced Technological Tools to Study Epigenetic Determinants of Metastasis. Front Genet 2020; 11:603552. [PMID: 33193750 PMCID: PMC7658393 DOI: 10.3389/fgene.2020.603552] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/09/2020] [Indexed: 12/11/2022] Open
Abstract
Metastasis is a complex process that involved in various genetic and epigenetic alterations during the progression of breast cancer. Recent evidences have indicated that the mutation in the genome sequence may not be the key factor for increasing metastatic potential. Epigenetic changes were revealed to be important for metastatic phenotypes transition with the development in understanding the epigenetic basis of breast cancer. Herein, we aim to present the potential epigenetic drivers that induce dysregulation of genes related to breast tumor growth and metastasis, with a particular focus on histone modification including histone acetylation and methylation. The pervasive role of major histone modification enzymes in cancer metastasis such as histone acetyltransferases (HAT), histone deacetylases (HDACs), DNA methyltransferases (DNMTs), and so on are demonstrated and further discussed. In addition, we summarize the recent advances of next-generation sequencing technologies and microfluidic-based devices for enhancing the study of epigenomic landscapes of breast cancer. This feature also introduces several important biotechnologists for identifying robust epigenetic biomarkers and enabling the translation of epigenetic analyses to the clinic. In summary, a comprehensive understanding of epigenetic determinants in metastasis will offer new insights of breast cancer progression and can be achieved in the near future with the development of innovative epigenomic mapping tools.
Collapse
Affiliation(s)
- Jialang Zhuang
- Biobank, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Qin Huo
- Biobank, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Fan Yang
- Biobank, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Ni Xie
- Biobank, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| |
Collapse
|
7
|
Deng C, Murphy TW, Zhang Q, Naler LB, Xu A, Lu C. Multiplexed and Ultralow-Input ChIP-seq Enabled by Tagmentation-Based Indexing and Facile Microfluidics. Anal Chem 2020; 92:13661-13666. [PMID: 32957776 DOI: 10.1021/acs.analchem.0c02550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Epigenome constitutes an important layer that regulates gene expression and dynamics during development and diseases. Extensive efforts have been made to develop epigenome profiling methods using a low number of cells and with high throughput. Chromatin immunoprecipitation (ChIP) is the most important approach for profiling genome-wide epigenetic changes such as histone modifications. In this report, we demonstrate microfluidic ChIPmentation (mu-CM), a microfluidic technology that enables profiling cell samples that individually do not generate enough ChIP DNA for sequencing library preparation. We used a simple microfluidic device to allow eight samples to be processed simultaneously. The samples were indexed differently using a tagmentation-based approach (ChIPmentation) and then merged for library preparation. A histone modification profile for each individual sample was obtained by demultiplexing the sequencing reads based on the indexes. Our technology allowed profiling 20 cells and is well suited for cell-type-specific studies using low-abundance tissues.
Collapse
Affiliation(s)
- Chengyu Deng
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Travis W Murphy
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Qiang Zhang
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Lynette B Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Alice Xu
- Blacksburg High School, Blacksburg, Virginia 24060, United States
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| |
Collapse
|
8
|
Xu Y, Doonan SR, Ordog T, Bailey RC. Translational Opportunities for Microfluidic Technologies to Enable Precision Epigenomics. Anal Chem 2020; 92:7989-7997. [PMID: 32496751 DOI: 10.1021/acs.analchem.0c01288] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Personalizing health care by taking genetic, environmental, and lifestyle factors into account is central to modern medicine. The crucial and pervasive roles epigenetic factors play in shaping gene-environment interactions are now well recognized. However, identifying robust epigenetic biomarkers and translating them to clinical tests has been difficult due in part to limitations of available platforms to detect epigenetic features genome-wide (epigenomic assays). This Feature introduces several important prospects for precision epigenomics, highlights capabilities and limitations of current laboratory technologies, and emphasizes opportunities for microfluidic tools to facilitate translation of epigenetic analyses to the clinic, with a particular focus on methods to profile gene-associated histone modifications and their impacts on chromatin structure and gene expression.
Collapse
Affiliation(s)
- Yi Xu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Steven R Doonan
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tamas Ordog
- Epigenomics Program, Center for Individualized Medicine, Department of Physiology and Biomedical Engineering, and Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Ryan C Bailey
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|