1
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Zhu F, Liu S, Bai X, Liu X, Lin B, Lu Y. Point‐of‐care multiplexed single‐cell protein secretion analysis based on tyramide signal amplification. VIEW 2022. [DOI: 10.1002/viw.20220033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Fengjiao Zhu
- Department of Biotechnology Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian China
- University of Chinese Academy of Sciences Beijing China
| | - Songnan Liu
- Department of Biotechnology Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian China
- University of Chinese Academy of Sciences Beijing China
| | - Xue Bai
- Department of Biotechnology Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian China
| | - Xianming Liu
- Department of Biotechnology Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian China
| | - Bingcheng Lin
- Department of Biotechnology Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian China
| | - Yao Lu
- Department of Biotechnology Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian China
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2
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Yan H, Ye Y, Zhao H, Zuo H, Li Y. Single-Cell RNA Sequencing for Analyzing the Intestinal Tract in Healthy and Diseased Individuals. Front Cell Dev Biol 2022; 10:915654. [PMID: 35874838 PMCID: PMC9300858 DOI: 10.3389/fcell.2022.915654] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
The intestinal tract is composed of different cell lineages with distinct functions and gene expression profiles, providing uptake of nutrients and protection against insults to the gut lumen. Changes in or damage to the cellulosity or local environment of the intestinal tract can cause various diseases. Single-cell RNA sequencing (scRNA-seq) is a powerful tool for profiling and analyzing individual cell data, making it possible to resolve rare and intermediate cell states that are hardly observed at the bulk level. In this review, we discuss the application of intestinal tract scRNA-seq in identifying novel cell subtypes and states, targets, and explaining the molecular mechanisms involved in intestinal diseases. Finally, we provide future perspectives on using single-cell techniques to discover molecular and cellular targets and biomarkers as a new approach for developing novel therapeutics for intestinal diseases.
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Affiliation(s)
- Hua Yan
- Department of Experimental Pathology, Beijing Institute of Radiation Medicine, Beijing, China
- The Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Yumeng Ye
- Department of Experimental Pathology, Beijing Institute of Radiation Medicine, Beijing, China
| | - HanZheng Zhao
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hongyan Zuo
- Department of Experimental Pathology, Beijing Institute of Radiation Medicine, Beijing, China
- Department of Pathology, Chengde Medical College, Chengde, China
- *Correspondence: Hongyan Zuo, ; Yang Li,
| | - Yang Li
- Department of Experimental Pathology, Beijing Institute of Radiation Medicine, Beijing, China
- Department of Pathology, Chengde Medical College, Chengde, China
- Academy of Life Sciences, Anhui Medical University, Hefei, China
- *Correspondence: Hongyan Zuo, ; Yang Li,
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3
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Angius A, Scanu AM, Arru C, Muroni MR, Carru C, Porcu A, Cossu-Rocca P, De Miglio MR. A Portrait of Intratumoral Genomic and Transcriptomic Heterogeneity at Single-Cell Level in Colorectal Cancer. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:1257. [PMID: 34833475 PMCID: PMC8624593 DOI: 10.3390/medicina57111257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 12/24/2022]
Abstract
In the study of cancer, omics technologies are supporting the transition from traditional clinical approaches to precision medicine. Intra-tumoral heterogeneity (ITH) is detectable within a single tumor in which cancer cell subpopulations with different genome features coexist in a patient in different tumor areas or may evolve/differ over time. Colorectal carcinoma (CRC) is characterized by heterogeneous features involving genomic, epigenomic, and transcriptomic alterations. The study of ITH is a promising new frontier to lay the foundation towards successful CRC diagnosis and treatment. Genome and transcriptome sequencing together with editing technologies are revolutionizing biomedical research, representing the most promising tools for overcoming unmet clinical and research challenges. Rapid advances in both bulk and single-cell next-generation sequencing (NGS) are identifying primary and metastatic intratumoral genomic and transcriptional heterogeneity. They provide critical insight in the origin and spatiotemporal evolution of genomic clones responsible for early and late therapeutic resistance and relapse. Single-cell technologies can be used to define subpopulations within a known cell type by searching for differential gene expression within the cell population of interest and/or effectively isolating signal from rare cell populations that would not be detectable by other methods. Each single-cell sequencing analysis is driven by clustering of cells based on their differentially expressed genes. Genes that drive clustering can be used as unique markers for a specific cell population. In this review we analyzed, starting from published data, the possible achievement of a transition from clinical CRC research to precision medicine with an emphasis on new single-cell based techniques; at the same time, we focused on all approaches and issues related to this promising technology. This transition might enable noninvasive screening for early diagnosis, individualized prediction of therapeutic response, and discovery of additional novel drug targets.
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Affiliation(s)
- Andrea Angius
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Cittadella Universitaria di Cagliari, 09042 Monserrato, Italy
| | - Antonio Mario Scanu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
| | - Caterina Arru
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.A.); (C.C.)
| | - Maria Rosaria Muroni
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
| | - Ciriaco Carru
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.A.); (C.C.)
| | - Alberto Porcu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
| | - Paolo Cossu-Rocca
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
| | - Maria Rosaria De Miglio
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
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4
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Breukers J, Horta S, Struyfs C, Spasic D, Feys HB, Geukens N, Thevissen K, Cammue BPA, Vanhoorelbeke K, Lammertyn J. Tuning the Surface Interactions between Single Cells and an OSTE+ Microwell Array for Enhanced Single Cell Manipulation. ACS APPLIED MATERIALS & INTERFACES 2021; 13:2316-2326. [PMID: 33411502 DOI: 10.1021/acsami.0c19657] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Retrieving single cells of interest from an array of microwells for further off-chip analysis is crucial in numerous biological applications. To this end, several single cell manipulation strategies have been developed, including optical tweezers (OT). OT represent a unique approach for contactless cell retrieval, but their performance is often suboptimal due to nonspecific cell adhesion to the microwell surface. In this study, we focused on improving the surface chemistry of microwell arrays to ensure efficient single cell manipulation using OT. For this purpose, the surface of an off-stoichiometry thiol-ene-epoxy (OSTE+) microwell array was grafted with polyethylene glycol (PEG) molecules with different molecular weights: PEG 360, PEG 500, PEG 2000, and a PEG Mix (an equimolar ratio of PEG 500 and PEG 2000). Contact angle measurements showed that the PEG grafting process resulted in an increased surface energy, which was stable for at least 16 weeks. Next, cell adhesion of two cell types, baker's yeast (Saccharomyces cerevisiae) and human B cells, to surfaces treated with different PEGs was evaluated by registering the presence of cellular motion inside microwells and the efficiency of optical lifting of cells that display motion. Optimal results were obtained for surfaces grafted with PEG 2000 and PEG Mix, reaching an average fraction of cells with motion of over 93% and an average lifting efficiency of over 96% for both cell types. Upon the integration of this microwell array with a polydimethylsiloxane (PDMS) microfluidic channel, PEG Mix resulted in proper washing of non-seeded cells. We further demonstrated the wide applicability of the platform by manipulating non-responding yeast cells to antifungal treatment and B cells expressing surface IgG antibodies. The combination of the optimized microwell surface with continuous microfluidics results in a powerful and versatile platform, allowing high-throughput single cell studies and retrieval of target cells for off-chip analysis.
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Affiliation(s)
- Jolien Breukers
- Department of Biosystems, Biosensors Group, KU Leuven, Willem De Croylaan 42, Leuven 3001, Belgium
| | - Sara Horta
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Etienne Sabbelaan 53, Kortrijk 8500, Belgium
| | - Caroline Struyfs
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Leuven 3001, Belgium
| | - Dragana Spasic
- Department of Biosystems, Biosensors Group, KU Leuven, Willem De Croylaan 42, Leuven 3001, Belgium
| | - Hendrik B Feys
- Transfusion Research Center, Belgian Red Cross-Flanders Ottergemsesteenweg 413, Gent 9000, Belgium
- Diagnostic Sciences, Ghent University, C. Heymanslaan 10, Gent 9000, Belgium
| | - Nick Geukens
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Karin Thevissen
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Leuven 3001, Belgium
| | - Bruno P A Cammue
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Leuven 3001, Belgium
| | - Karen Vanhoorelbeke
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Etienne Sabbelaan 53, Kortrijk 8500, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, Willem De Croylaan 42, Leuven 3001, Belgium
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5
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Prakash S, Ashley BK, Doyle PS, Hassan U. Design of a Multiplexed Analyte Biosensor using Digital Barcoded Particles and Impedance Spectroscopy. Sci Rep 2020; 10:6109. [PMID: 32273525 PMCID: PMC7145859 DOI: 10.1038/s41598-020-62894-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/18/2020] [Indexed: 02/06/2023] Open
Abstract
Multiplexing allows quantifying multiple analytes in a single step, providing advantages over individual testing through shorter processing time, lower sample volume, and reduced cost per test. Currently, flow cytometry is the gold standard for biomedical multiplexing, but requires technical training, extensive data processing, and expensive operational and capital costs. To solve this challenge, we designed digital barcoded particles and a microfluidic architecture for multiplexed analyte quantification. In this work, we simulate and model non-fluorescence-based microfluidic impedance detection with a single excitation and detection scheme using barcoded polymer microparticles. Our barcoded particles can be designed with specific coding regions and generate numerous distinct patterns enabling digital barcoding. We found that signals based on adhered microsphere position and relative orientation were evaluated and separated based on their associated electrical signatures and had a 7 µm microsphere limit of detection. Our proposed microfluidic system can enumerate micron-sized spheres in a single assay using barcoded particles of various configurations. As representation of blood cells, the microsphere concentrations may provide useful information on disease onset and progression. Such sensors may be used for diagnostic and management of common critical care diseases like sepsis, acute kidney injury, urinary tract infections, and HIV/AIDS.
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Affiliation(s)
- Shreya Prakash
- Department of Electrical and Computer Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Brandon K Ashley
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Patrick S Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Umer Hassan
- Department of Electrical and Computer Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
- Global Health Institute, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
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6
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Liu M, Jin M, Li L, Ji Y, Zhu F, Luo Y, Liu T, Lin B, Lu Y. PDMS Microwell Stencil Based Multiplexed Single‐Cell Secretion Analysis. Proteomics 2020; 20:e1900231. [DOI: 10.1002/pmic.201900231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/13/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Meimei Liu
- Department of Materials Science and EngineeringDalian Maritime University Dalian 116026 China
- Department of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
| | - Meihua Jin
- Department of Materials Science and EngineeringDalian Maritime University Dalian 116026 China
| | - Linmei Li
- Department of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
| | - Yahui Ji
- Department of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
| | - Fengjiao Zhu
- Department of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
| | - Yong Luo
- State Key Laboratory of Fine ChemicalsDepartment of Chemical EngineeringDalian University of Technology Dalian 116024 China
| | - Tingjiao Liu
- College of StomatologyDalian Medical University Dalian 116044 China
| | - Bingcheng Lin
- Department of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
| | - Yao Lu
- Department of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
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7
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Kshitiz, Ellison DD, Suhail Y, Afzal J, Woo L, Kilic O, Spees J, Levchenko A. Dynamic secretome of bone marrow-derived stromal cells reveals a cardioprotective biochemical cocktail. Proc Natl Acad Sci U S A 2019; 116:14374-14383. [PMID: 31239339 PMCID: PMC6628676 DOI: 10.1073/pnas.1902598116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Transplanted stromal cells have demonstrated considerable promise as therapeutic agents in diverse disease settings. Paracrine signaling can be an important mediator of these therapeutic effects at the sites of acute or persistent injury and inflammation. As many stromal cell types, including bone marrow-derived stromal cells (BMSCs), display tissue-specific responses, there is a need to explore their secretory dynamics in the context of tissue and injury type. Paracrine signals are not static, and could encode contextual dynamics in the kinetic changes of the concentrations of the secreted ligands. However, precise measurement of dynamic and context-specific cellular secretory signatures, particularly in adherent cells, remains challenging. Here, by creating an experimental and computational analysis platform, we reconstructed dynamic secretory signatures of cells based on a very limited number of time points. By using this approach, we demonstrate that the secretory signatures of CD133-positive BMSCs are uniquely defined by distinct biological contexts, including signals from injured cardiac cells undergoing oxidative stress, characteristic of cardiac infarction. Furthermore, we show that the mixture of recombinant factors reproducing the dynamics of BMSC-generated secretion can mediate a highly effective rescue of cells injured by oxidative stress and an improved cardiac output. These results support the importance of the dynamic multifactorial paracrine signals in mediating remedial effects of stromal stem cells, and pave the way for stem cell-inspired cell-free treatments of cardiac and other injuries.
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Affiliation(s)
- Kshitiz
- Yale Institute of Systems Biology, Yale University, West Haven, CT 06516;
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT 06030
| | - David D Ellison
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Yasir Suhail
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT 06030
| | - Junaid Afzal
- Department of Cardiology, University of California, San Francisco, CA 94115
| | - Laura Woo
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Onur Kilic
- Yale Institute of Systems Biology, Yale University, West Haven, CT 06516
| | - Jeffrey Spees
- Department of Cellular Molecular and Biomedical Sciences, University of Vermont, Burlington, VT 05405
| | - Andre Levchenko
- Yale Institute of Systems Biology, Yale University, West Haven, CT 06516;
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8
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Fisher RC, Bellamkonda K, Alex Molina L, Xiang S, Liska D, Sarvestani SK, Chakrabarti S, Berg A, Jorgensen ML, Hatala D, Chen S, Aiello A, Appelman HD, Scott EW, Huang EH. Disrupting Inflammation-Associated CXCL8-CXCR1 Signaling Inhibits Tumorigenicity Initiated by Sporadic- and Colitis-Colon Cancer Stem Cells. Neoplasia 2019; 21:269-281. [PMID: 30738331 PMCID: PMC6370871 DOI: 10.1016/j.neo.2018.12.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/18/2018] [Accepted: 12/22/2018] [Indexed: 02/07/2023] Open
Abstract
Dysfunctional inflammatory pathways are associated with an increased risk of cancer, including colorectal cancer. We have previously identified and enriched for a self-renewing, colon cancer stem cell (CCSC) subpopulation in primary sporadic colorectal cancers (CRC) and a related subpopulation in ulcerative colitis (UC) patients defined by the stem cell marker, aldehyde dehydrogenase (ALDH). Subsequent work demonstrated that CCSC-initiated tumors are dependent on the inflammatory chemokine, CXCL8, a known inducer of tumor proliferation, angiogenesis and invasion. Here, we use RNA interference to target CXCL8 and its receptor, CXCR1, to establish the existence of a functional signaling pathway promoting tumor growth initiated by sporadic and colitis CCSCs. Knocking down either CXCL8 or CXCR1 had a dramatic effect on inhibiting both in vitro proliferation and angiogenesis. Likewise, tumorigenicity was significantly inhibited due to reduced levels of proliferation and angiogenesis. Decreased expression of cycle cell regulators cyclins D1 and B1 along with increased p21 levels suggested that the reduction in tumor growth is due to dysregulation of cell cycle progression. Therapeutically targeting the CXCL8-CXCR1 signaling pathway has the potential to block sustained tumorigenesis by inhibiting both CCSC- and pCCSC-induced proliferation and angiogenesis.
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Affiliation(s)
- Robert C Fisher
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kishan Bellamkonda
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - L Alex Molina
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Shao Xiang
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - David Liska
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Department of Colorectal Surgery, Cleveland Clinic, Cleveland, OH, USA
| | - Samaneh K Sarvestani
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - Annamarie Berg
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Marda L Jorgensen
- Department of Pediatrics, University of Florida, Gainesville, Florida, USA
| | - Denise Hatala
- Immunochemistry Core, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Sugong Chen
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Alexandra Aiello
- Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Henry D Appelman
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Edward W Scott
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Emina H Huang
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Department of Colorectal Surgery, Cleveland Clinic, Cleveland, OH, USA.
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9
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Herrera V, Hsu SCJ, Rahim MK, Chen C, Nguyen L, Liu WF, Haun JB. Pushing the limits of detection for proteins secreted from single cells using quantum dots. Analyst 2019; 144:980-989. [PMID: 30270391 PMCID: PMC6349524 DOI: 10.1039/c8an01083h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Single cell analysis methods are increasingly being utilized to investigate how individual cells process information and respond to diverse stimuli. Soluble proteins play a critical role in controlling cell populations and tissues, but directly monitoring secretion is technically challenging. Microfabricated well arrays have been developed to assess secretion at the single cell level, but these systems are limited by low detection sensitivity. Semiconductor quantum dots (QD) exhibit remarkably bright and photostable luminescence signal, but to date they have not been evaluated in single cell secretion studies using microfabricated well arrays. Here, we used QDs in a sandwich immunoassay to detect secretion of the soluble cytokine tumor necrosis factor-α (TNF-α) from single cells. To enhance detection sensitivity, we employed two different strategies. First, we used a unique single QD imaging approach, which provided a detection threshold (180 attomolar) that was >100-fold lower than previously reported results using QDs. We also amplified QD binding to each captured TNF-α molecule using the bioorthogonal cycloaddition reaction between trans-cyclooctene and tetrazine, which further lowered detection threshold to 60 attomolar. This is 6 orders of magnitude more sensitive than organic fluorophores that have been used for single cell secretion studies, and far surpasses single molecule resolution within sub-picoliter microwells that are used to assess single cell secretion. Finally, single cell secretion studies were performed using phorbol 12-myristate 13-acetate (PMA) differentiated and lipopolysaccharide (LPS) activated U-937 cells. TNF-α secretion was detected from 3-fold more single cells using the QD-based method in comparison to rhodamine, which was accomplished by extending sensitivity into the range of ∼2 to 10 000 molecules captured per microwell. In future work, we will apply this technique to assess immune cell secretion dynamics under diverse stimuli and disease settings. We will also incorporate multiplexing capabilities to evaluate the secretome at the resolution of single molecules.
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Affiliation(s)
- Vanessa Herrera
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA.
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10
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Nelep C, Eberhardt J. Automated rare single cell picking with the ALS cellcelector™. Cytometry A 2018; 93:1267-1270. [PMID: 30184320 PMCID: PMC6586056 DOI: 10.1002/cyto.a.23568] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/19/2018] [Accepted: 06/28/2018] [Indexed: 01/02/2023]
Abstract
Molecular analysis of rare single cells like circulating tumor cells (CTCs) from whole blood patient samples bears multiple challenges. One of those challenges is the efficient and ideally loss-free isolation of CTCs over contaminating white and red blood cells. While there is a multitude of commercial and non-commercial systems available for the enrichment of CTCs their cell output does not deliver the purity most molecular analysis methods require. Here we describe the ALS CellCelector™ which can solve this challenge allowing the retrieval of 100% pure single CTCs from blood processed by different upstream enrichment techniques. It is a multifunctional, extremely flexible system for automated screening of cell culture plates, Petri dishes, and microscope slides. Fixed or live single cells or multicellular clusters detected during screening can be picked out of those plates automatically. The complete scan and picking process is fully documented hence allowing highest standardization and reproducibility of all processes. Use of CellCelector allowed the isolation of pure single tumor cells or clusters from liquid biopsies of breast, prostate, ovarian, colorectal, lung, and brain cancers for their subsequent molecular analysis. © 2018 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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11
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Abstract
Therapeutics that block kinases, transcriptional modifiers, immune checkpoints and other biological vulnerabilities are transforming cancer treatment. As a result, many patients achieve dramatic responses, including complete radiographical or pathological remission, yet retain minimal residual disease (MRD), which results in relapse. New functional approaches can characterize clonal heterogeneity and predict therapeutic sensitivity of MRD at a single-cell level. Preliminary evidence suggests that iterative detection, profiling and targeting of MRD would meaningfully improve outcomes and may even lead to cure.
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Affiliation(s)
- Marlise R. Luskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA,
| | - Mark A. Murakami
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA,
| | - Scott R. Manalis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA
- Corresponding authors: (S. R. M.) and (D. M. W.)
| | - David M. Weinstock
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA,
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, 02142, USA
- Corresponding authors: (S. R. M.) and (D. M. W.)
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12
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Abstract
Quantification of single-cell proteomics provides key insights in the field of cellular heterogeneity. This chapter discusses the emerging techniques that are being used to measure the protein copy numbers at the single-cell level, which includes flow cytometry, mass cytometry, droplet cytometry, microengraving, and single-cell barcoding microchip. The advantages and limitations of each technique are compared, and future research opportunities are highlighted.
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13
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Yeo T, Tan SJ, Lim CL, Lau DPX, Chua YW, Krisna SS, Iyer G, Tan GS, Lim TKH, Tan DS, Lim WT, Lim CT. Microfluidic enrichment for the single cell analysis of circulating tumor cells. Sci Rep 2016; 6:22076. [PMID: 26924553 PMCID: PMC4770429 DOI: 10.1038/srep22076] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/05/2016] [Indexed: 12/18/2022] Open
Abstract
Resistance to drug therapy is a major concern in cancer treatment. To probe clones resistant to chemotherapy, the current approach is to conduct pooled cell analysis. However, this can yield false negative outcomes, especially when we are analyzing a rare number of circulating tumor cells (CTCs) among an abundance of other cell types. Here, we develop a microfluidic device that is able to perform high throughput, selective picking and isolation of single CTC to 100% purity from a larger population of other cells. This microfluidic device can effectively separate the very rare CTCs from blood samples from as few as 1 in 20,000 white blood cells. We first demonstrate isolation of pure tumor cells from a mixed population and track variations of acquired T790M mutations before and after drug treatment using a model PC9 cell line. With clinical CTC samples, we then show that the isolated single CTCs are representative of dominant EGFR mutations such as T790M and L858R found in the primary tumor. With this single cell recovery device, we can potentially implement personalized treatment not only through detecting genetic aberrations at the single cell level, but also through tracking such changes during an anticancer therapy.
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Affiliation(s)
- Trifanny Yeo
- Clearbridge Accelerator Pte Ltd, 81 Science Park Drive, The Chadwick, #02-03, Singapore Science Park 1, Singapore 118257, Singapore
| | - Swee Jin Tan
- Clearbridge Accelerator Pte Ltd, 81 Science Park Drive, The Chadwick, #02-03, Singapore Science Park 1, Singapore 118257, Singapore
| | - Chew Leng Lim
- School of Biological Science, National Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Dawn Ping Xi Lau
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore
| | - Yong Wei Chua
- Department of Pathology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
| | - Sai Sakktee Krisna
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore
| | - Gopal Iyer
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore
| | - Gek San Tan
- Department of Pathology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
| | - Tony Kiat Hon Lim
- Department of Pathology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
| | - Daniel S.W. Tan
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore
- Cancer Stem Cell Biology, Genome Institute of Singapore, 60 Biopolis St, #02-01, 138672, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore
| | - Wan-Teck Lim
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore
- Duke-NUS Medical School, 8 College Road, 169857, Singapore
- Institute of Molecular and Cell Biology, A*Star, 61 Biopolis Drive Proteos, 138673, Singapore
| | - Chwee Teck Lim
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Block E4, #04-08, Singapore 117583, Singapore
- Mechanobiology Institute of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore
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14
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Development of Microfluidic Systems Enabling High-Throughput Single-Cell Protein Characterization. SENSORS 2016; 16:232. [PMID: 26891303 PMCID: PMC4801608 DOI: 10.3390/s16020232] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 01/21/2016] [Accepted: 02/02/2016] [Indexed: 01/09/2023]
Abstract
This article reviews recent developments in microfluidic systems enabling high-throughput characterization of single-cell proteins. Four key perspectives of microfluidic platforms are included in this review: (1) microfluidic fluorescent flow cytometry; (2) droplet based microfluidic flow cytometry; (3) large-array micro wells (microengraving); and (4) large-array micro chambers (barcode microchips). We examine the advantages and limitations of each technique and discuss future research opportunities by focusing on three key performance parameters (absolute quantification, sensitivity, and throughput).
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15
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Avesar J, Arye TB, Levenberg S. Frontier microfluidic techniques for short and long-term single cell analysis. LAB ON A CHIP 2014; 14:2161-7. [PMID: 24671389 DOI: 10.1039/c4lc00013g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Here, we review the frontier microfluidic techniques for single cell analysis (SCA), which is important for research of many biological systems. Microfluidics provides high-throughput, high-resolution experiments at low cost and reagent use, making it especially useful for single cell analysis. Recent advancements in the field have made SCA more feasible, improving device throughput and resolution, adding capabilities, and combining different functions to bring forth new assays. Developments in incubation have allowed for long-term cell tracking assays to be performed with single cell resolution. The ability of systems to provide chemical isolation or prolonged growth of adherent cells is also discussed.
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Affiliation(s)
- Jonathan Avesar
- Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel 32000.
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16
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Adalsteinsson VA, Love JC. Towards Engineered Processes for Sequencing-Based Analysis of Single Circulating Tumor Cells. Curr Opin Chem Eng 2014; 4:97-104. [PMID: 24839591 DOI: 10.1016/j.coche.2014.01.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Sequencing-based analysis of single circulating tumor cells (CTCs) has the potential to revolutionize our understanding of metastatic cancer and improve clinical care. Technologies exist to enrich, identify, recover, and sequence single cells, but to enable systematic routine analysis of single CTCs from a range of cancer patients, there is a need to establish processes that efficiently integrate these specific operations. Such engineered processes should address challenges associated with the yield and viability of enriched CTCs, the robust identification of candidate single CTCs with minimal degradation of DNA, the bias in whole-genome amplification, and the efficient handling of candidate single CTCs or their amplified DNA products. Advances in methods for single-cell analysis and nanoscale technologies suggest opportunities to overcome these challenges, and could create integrated platforms that perform several of the unit operations together. Ultimately, technologies should be selected or adapted for optimal performance and compatibility in an integrated process.
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Affiliation(s)
- Viktor A Adalsteinsson
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA ; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA ; The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02412, USA
| | - J Christopher Love
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA ; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA ; The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02412, USA
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