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Ahuja K, Rather GM, Lin Z, Sui J, Xie P, Le T, Bertino JR, Javanmard M. Toward point-of-care assessment of patient response: a portable tool for rapidly assessing cancer drug efficacy using multifrequency impedance cytometry and supervised machine learning. MICROSYSTEMS & NANOENGINEERING 2019; 5:34. [PMID: 31645995 PMCID: PMC6799891 DOI: 10.1038/s41378-019-0073-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 01/31/2019] [Accepted: 03/25/2019] [Indexed: 05/07/2023]
Abstract
We present a novel method to rapidly assess drug efficacy in targeted cancer therapy, where antineoplastic agents are conjugated to antibodies targeting surface markers on tumor cells. We have fabricated and characterized a device capable of rapidly assessing tumor cell sensitivity to drugs using multifrequency impedance spectroscopy in combination with supervised machine learning for enhanced classification accuracy. Currently commercially available devices for the automated analysis of cell viability are based on staining, which fundamentally limits the subsequent characterization of these cells as well as downstream molecular analysis. Our approach requires as little as 20 μL of volume and avoids staining allowing for further downstream molecular analysis. To the best of our knowledge, this manuscript presents the first comprehensive attempt to using high-dimensional data and supervised machine learning, particularly phase change spectra obtained from multi-frequency impedance cytometry as features for the support vector machine classifier, to assess viability of cells without staining or labelling.
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Affiliation(s)
- Karan Ahuja
- Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ USA
| | - Gulam M. Rather
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ USA
| | - Zhongtian Lin
- Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ USA
| | - Jianye Sui
- Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ USA
| | - Pengfei Xie
- Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ USA
| | - Tuan Le
- Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ USA
| | - Joseph R. Bertino
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ USA
| | - Mehdi Javanmard
- Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ USA
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Affiliation(s)
- Gongchen Sun
- School of Chemical & Biomolecular Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Hang Lu
- School of Chemical & Biomolecular Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
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4
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Drug screening of cancer cell lines and human primary tumors using droplet microfluidics. Sci Rep 2017; 7:9109. [PMID: 28831060 PMCID: PMC5567315 DOI: 10.1038/s41598-017-08831-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/19/2017] [Indexed: 01/23/2023] Open
Abstract
Precision Medicine in Oncology requires tailoring of therapeutic strategies to individual cancer patients. Due to the limited quantity of tumor samples, this proves to be difficult, especially for early stage cancer patients whose tumors are small. In this study, we exploited a 2.4 × 2.4 centimeters polydimethylsiloxane (PDMS) based microfluidic chip which employed droplet microfluidics to conduct drug screens against suspended and adherent cancer cell lines, as well as cells dissociated from primary tumor of human patients. Single cells were dispersed in aqueous droplets and imaged within 24 hours of drug treatment to assess cell viability by ethidium homodimer 1 staining. Our results showed that 5 conditions could be screened for every 80,000 cells in one channel on our chip under current circumstances. Additionally, screening conditions have been adapted to both suspended and adherent cancer cells, giving versatility to potentially all types of cancers. Hence, this study provides a powerful tool for rapid, low-input drug screening of primary cancers within 24 hours after tumor resection from cancer patients. This paves the way for further technological advancement to cutting down sample size and increasing drug screening throughput in advent to personalized cancer therapy.
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Prakadan SM, Shalek AK, Weitz DA. Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices. Nat Rev Genet 2017; 18:345-361. [PMID: 28392571 DOI: 10.1038/nrg.2017.15] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recent advances in cellular profiling have demonstrated substantial heterogeneity in the behaviour of cells once deemed 'identical', challenging fundamental notions of cell 'type' and 'state'. Not surprisingly, these findings have elicited substantial interest in deeply characterizing the diversity, interrelationships and plasticity among cellular phenotypes. To explore these questions, experimental platforms are needed that can extensively and controllably profile many individual cells. Here, microfluidic structures - whether valve-, droplet- or nanowell-based - have an important role because they can facilitate easy capture and processing of single cells and their components, reducing labour and costs relative to conventional plate-based methods while also improving consistency. In this article, we review the current state-of-the-art methodologies with respect to microfluidics for mammalian single-cell 'omics' and discuss challenges and future opportunities.
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Affiliation(s)
- Sanjay M Prakadan
- Institute for Medical Engineering &Science (IMES) and Department of Chemistry, MIT, Cambridge, Massachusetts 02139, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Alex K Shalek
- Institute for Medical Engineering &Science (IMES) and Department of Chemistry, MIT, Cambridge, Massachusetts 02139, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - David A Weitz
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
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Weber RJ, Cerchiari AE, Delannoy LS, Garbe JC, LaBarge MA, Desai TA, Gartner ZJ. Rapid Organoid Reconstitution by Chemical Micromolding. ACS Biomater Sci Eng 2016; 2:1851-1855. [DOI: 10.1021/acsbiomaterials.6b00421] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Robert J. Weber
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, California 94158, United States,
- Chemistry
and Chemical Biology Graduate Program, University of California, San Francisco, 600 16th Street, Room 522, San Francisco, California 94158, United States,
- Medical
Scientist Training Program, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, United States
| | - Alec E. Cerchiari
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, California 94158, United States,
- UC Berkeley−UCSF Group in Bioengineering, 1700 Fourth Street, Room 216, San Francisco, California 94158, United States,
- UCSF Bioengineering and Therapeutic Sciences, 1700 Fourth Street, Room 216B, San Francisco, California 94158, United States
| | - Lucas S. Delannoy
- Laboratory
of Stem Cell Bioengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Station
15, Building Al 1106, CH-1015 Lausanne, Switzerland
| | - James C. Garbe
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, California 94158, United States,
- Life
Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Mark A. LaBarge
- Life
Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Tejal A. Desai
- UC Berkeley−UCSF Group in Bioengineering, 1700 Fourth Street, Room 216, San Francisco, California 94158, United States,
- UCSF Bioengineering and Therapeutic Sciences, 1700 Fourth Street, Room 216B, San Francisco, California 94158, United States
| | - Zev J. Gartner
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, California 94158, United States,
- Chemistry
and Chemical Biology Graduate Program, University of California, San Francisco, 600 16th Street, Room 522, San Francisco, California 94158, United States,
- UC Berkeley−UCSF Group in Bioengineering, 1700 Fourth Street, Room 216, San Francisco, California 94158, United States,
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