Microfluidic platform for multiplexed detection in single cells and methods thereof

Wu, Meiye; Singh, Anup K.

Title: Microfluidic platform for multiplexed detection in single cells and methods thereof

Abstract

The present invention relates to a microfluidic device and platform configured to conduct multiplexed analysis within the device. In particular, the device allows multiple targets to be detected on a single-cell level. Also provided are methods of performing multiplexed analyses to detect one or more target nucleic acids, proteins, and post-translational modifications.

Inventors:: Wu, Meiye; Singh, Anup K.

Issue Date:: 2020-08-04

Research Org.:: Sandia National Lab. (SNL-CA), Livermore, CA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1735100

Patent Number(s):: 10731205

Application Number:: 15/925,389

Assignee:: National Technology & Engineering Solutions of Sandia, LLC (Albuquerque, NM)

Patent Classifications (CPCs):: B - PERFORMING OPERATIONS B01 - PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL B01L - CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE

C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS

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B - PERFORMING OPERATIONS B01 - PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL B01L - CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
B01L3/502776 - {specially adapted for focusing or laminating flows}

C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
C12Q1/6804 - Nucleic acid analysis using immunogens
C12Q1/6816 - characterised by the detection means
C12Q1/6837 - using probe arrays or probe chips
C12Q1/6841 - In situ hybridisation
C12Q1/6844 - Nucleic acid amplification reactions
C12Q2537/143 - Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
C12Q2565/629 - being a microfluidic device

C - CHEMISTRY C40 - COMBINATORIAL TECHNOLOGY C40B - COMBINATORIAL CHEMISTRY
C40B30/04 - by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding

G - PHYSICS G01 - MEASURING G01N - INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
G01N15/1459 - {the analysis being performed on a sample stream}
G01N15/1484 - {microstructural devices}
G01N2015/1006 - {for cytology}
G01N33/536 - with immune complex formed in liquid phase

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DOE Contract Number:: NA0003525

Resource Type:: Patent

Resource Relation:: Patent File Date: 03/19/2018

Country of Publication:: United States

Language:: English

Subject:: 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Wu, Meiye, and Singh, Anup K. Microfluidic platform for multiplexed detection in single cells and methods thereof.  United States: N. p., 2020. 
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                    Wu, Meiye, & Singh, Anup K. Microfluidic platform for multiplexed detection in single cells and methods thereof.  United States.

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                    Wu, Meiye, and Singh, Anup K. Tue .  
        "Microfluidic platform for multiplexed detection in single cells and methods thereof".  United States.  https://www.osti.gov/servlets/purl/1735100.

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@article{osti_1735100,

  title        = {Microfluidic platform for multiplexed detection in single cells and methods thereof},

  author       = {Wu, Meiye and Singh, Anup K.},

  abstractNote = {The present invention relates to a microfluidic device and platform configured to conduct multiplexed analysis within the device. In particular, the device allows multiple targets to be detected on a single-cell level. Also provided are methods of performing multiplexed analyses to detect one or more target nucleic acids, proteins, and post-translational modifications.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {2020},

  month        = {8}

}

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System and method for multiple laser triggering
patent-application, July 2005

Auer, Robert Edward; Lew, Clarence; Pentoney, Stephen Lyle
US Patent Document 10/763652; 20050162648
URL: https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20050162648

Devices, systems, and methods for conducting sandwich assays using sedimentation
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Schaff, Ulrich Y.; Sommer, Gregory J.; Singh, Anup K.
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MicroRNA In Situ Hybridization
book, December 2011

Nielsen, Boye Schnack; Fan, Jian-Bing
Next-Generation MicroRNA Expression Profiling Technology, p. 67-84
https://doi.org/10.1007/978-1-61779-427-8_5

Fluid Delivery Manifolds and Microfluidic Systems
patent-application, April 2012

Renzi, Ronald F.; Sommer, Gregory J.; Singh, Anup K.
US Patent Document 12/900276; 20120085644
URL: https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20120085644

Electrokinetic concentration of charged molecules
patent, August 2002

Singh, Anup K.; Neyer, David W.; Schoeniger, Joseph S.
US Patent Document 6,428,666
URL: https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/6428666

Single-cell protein analysis
journal, February 2012

Wu, Meiye; Singh, Anup K.
Current Opinion in Biotechnology, Vol. 23, Issue 1, p. 83-88
https://doi.org/10.1016/j.copbio.2011.11.023

Dielectrokinetic chromatography devices
patent, December 2014

Chirica, Gabriela S.; Fiechtner, Gregory J.; Singh, Anup K.
US Patent Document 8,911,606
URL: https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/8911606

Microfluidic devices and methods including porous polymer monoliths
patent, December 2015

Hatch, Anson V.; Sommer, Gregory J.; Singh, Anup K.
US Patent Document 9,201,069
URL: https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/9201069

Microfluidic Chip for High-Throughput Perfusion-Based Three-Dimensional Cell Culture
patent-application, September 2012

Wu, Min-Hsien; Wang, Shih-Siou; Tsai, Wan-Chen
US Patent Application 13/241123; 20120231976
URL: https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20120231976

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Title: Microfluidic platform for multiplexed detection in single cells and methods thereof

Abstract

Citation Formats

Microfluidic fluorescence in situ hybridization and flow cytometry (μFlowFISH) journal, January 2011

Devices and Methods for Pharmacokinetic-Based Cell Culture System patent-application, August 2012

On-chip cell migration detection patent-application, October 2009

Locked Nucleic Acid and Flow Cytometry-Fluorescence In Situ Hybridization for the Detection of Bacterial Small Noncoding RNAs journal, November 2011

Proximity ligation assays for sensitive and specific protein analyses journal, October 2005

Microfluidic devices, systems, and methods for quantifying particles using centrifugal force patent, November 2015

Microfluidic devices and methods for integrated flow cytometry patent, August 2011

Method for analyte detection using proximity probes patent, September 2012

Nuclear translocation kinetics of NF-κB in macrophages challenged with pathogens in a microfluidic platform journal, January 2009

Analyzer and particle imaging method patent, March 2014

Microfluidic Platforms for Single-Cell Protein Analysis journal, December 2013

Microfluidic device having an immobilized pH gradient and page gels for protein separation and analysis patent, May 2014

Monitoring viral RNA in infected cells with LNA flow-FISH journal, June 2010

Methods, microfluidic devices, and systems for detection of an active enzymatic agent patent, October 2014

Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq journal, June 2010

Single cell genome sequencing journal, June 2012

Dielectrokinetic chromatography and devices thereof patent, April 2014

CD69 and Regulatiof the Immune Function journal, January 1999

Global quantitative phosphoprotein analysis using Multiplexed Proteomics technology journal, July 2003

Single Cell Profiling of Circulating Tumor Cells: Transcriptional Heterogeneity and Diversity from Breast Cancer Cell Lines journal, May 2012

LNA flow–FISH: A flow cytometry–fluorescence in situ hybridization method to detect messenger RNA using locked nucleic acid probes journal, July 2009

Cytokine detection by antibody-based proximity ligation journal, May 2004

Method for dialysis on microchips using thin porous polymer membrane patent, May 2009

A custom microarray platform for analysis of microRNA gene expression journal, September 2004

Direct observation of individual endogenous protein complexes in situ by proximity ligation journal, October 2006

Rolling circle replication of padlock probes patent, July 2006

CD69 Association with Jak3/Stat5 Proteins Regulates Th17 Cell Differentiation journal, August 2010

Apparatus for DNA sequencing patent, October 2001

Single-cell gene-expression profiling reveals qualitatively distinct CD8 T cells elicited by different gene-based vaccines journal, March 2011

Sterile flow cytometer and sorter with mechanical isolation between flow chamber and sterile enclosure patent, June 1997

The first analogues of LNA (Locked Nucleic Acids): Phosphorothioate-LNA and 2′-thio-LNA journal, August 1998

A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA) journal, March 2006

Fully Integrated Microfluidic Platform Enabling Automated Phosphoprofiling of Macrophage Response journal, May 2009

Obtaining information from optical cavity output light patent, March 2009

Miniaturized cytometer for detecting multiple species in a sample patent-application, May 2005

Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes journal, December 2004

Microchannel gel electrophoretic separation systems and methods for preparing and using patent, February 2015

Microfluidically-unified cell culture, sample preparation, imaging and flow cytometry for measurement of cell signaling pathways with single cell resolution journal, January 2012

Method for forming polymerized microfluidic devices patent, November 2011

System for concentrating and analyzing particles suspended in a fluid patent, April 2011

miRNA Detection at Single-Cell Resolution Using Microfluidic LNA Flow-FISH book, January 2014

Isotropically etched radial micropore for cell concentration, immobilization, and picodroplet generation journal, January 2009

Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs journal, November 2005

Devices, systems, and methods for microscale isoelectric fractionation patent, August 2016

Dielectrophoretic systems without embedded electrodes patent, March 2006

Rolling circle replication of padlock probes patent, May 2003

Foxp3-Dependent MicroRNA155 Confers Competitive Fitness to Regulatory T Cells by Targeting SOCS1 Protein journal, January 2009

Method for voltage-gated protein fractionation patent, April 2012

Microfluidic Molecular Assay Platform for the Detection of miRNAs, mRNAs, Proteins, and Posttranslational Modifications at Single-Cell Resolution journal, December 2014

Devices, systems, and methods for microscale isoelectric fractionation patent, April 2015

Dialysis membrane for separation on microchips patent, July 2010

Microfluidic devices and methods including porous polymer monoliths patent, April 2014

Microfluidic Platform For Cell Culture And Assay patent-application, June 2011

Regulation of the Germinal Center Response by MicroRNA-155 journal, April 2007

Immuno-polymerase chain reaction system for antigen detection patent, September 1997

Absolute quantitation of microRNAs with a PCR-based assay journal, December 2006

Portable modular detection system patent, October 2009

Method for forming polymerized microfluidic devices patent, March 2013

Single-Cell Measurements of IgE-Mediated FcεRI Signaling Using an Integrated Microfluidic Platform journal, March 2013

Microfluidic-Based Cell Sorting of Francisella tularensis Infected Macrophages Using Optical Forces journal, August 2008

FISHing with locked nucleic acids (LNA): evaluation of different LNA/DNA mixmers journal, August 2003

Microchannel gel electrophoretic separation systems and methods for preparing and using patent, September 2013

Microfluidic device having an immobilized pH gradient and PAGE gels for protein separation and analysis patent, December 2012

Dialysis on microchips using thin porous polymer membranes patent, September 2007

Arrays, Substrates, Devices, Methods And Systems For Detecting Target Molecules patent-application, February 2009

Single Cell MicroRNA Analysis Using Microfluidic Flow Cytometry journal, January 2013

MicroRNA expression profiling of single whole embryonic stem cells journal, January 2006

Rapid in situ codetection of noncoding RNAs and proteins in cells and formalin-fixed paraffin-embedded tissue sections without protease treatment journal, May 2010

In Situ Proximity Ligation Assay for Microscopy and Flow Cytometry journal, April 2011

Preconcentration and separation of analytes in microchannels patent, November 2010

Ultrasensitive immunoassays patent, April 2005

Systems, devices, and methods for agglutination assays using sedimentation patent, January 2016

Sol-gel method for encapsulating molecules patent, December 2002

Microwell cell-culture device and fabrication method patent, September 2012

Bringing chemistry to life journal, August 2011

Multi-analyte analysis of saliva biomarkers as predictors of periodontal and pre-implant disease patent, April 2015

Multiplexed Proximity Ligation Assay patent-application, July 2014

Microfluidic fluorescence in situ hybridization and flow cytometry (μFlowFISH)
journal, January 2011

Devices and Methods for Pharmacokinetic-Based Cell Culture System
patent-application, August 2012

On-chip cell migration detection
patent-application, October 2009

Locked Nucleic Acid and Flow Cytometry-Fluorescence In Situ Hybridization for the Detection of Bacterial Small Noncoding RNAs
journal, November 2011

Proximity ligation assays for sensitive and specific protein analyses
journal, October 2005

Microfluidic devices, systems, and methods for quantifying particles using centrifugal force
patent, November 2015

Microfluidic devices and methods for integrated flow cytometry
patent, August 2011

Method for analyte detection using proximity probes
patent, September 2012

Nuclear translocation kinetics of NF-κB in macrophages challenged with pathogens in a microfluidic platform
journal, January 2009

Analyzer and particle imaging method
patent, March 2014

Microfluidic Platforms for Single-Cell Protein Analysis
journal, December 2013

Microfluidic device having an immobilized pH gradient and page gels for protein separation and analysis
patent, May 2014

Monitoring viral RNA in infected cells with LNA flow-FISH
journal, June 2010

Methods, microfluidic devices, and systems for detection of an active enzymatic agent
patent, October 2014

Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq
journal, June 2010

Single cell genome sequencing
journal, June 2012

Dielectrokinetic chromatography and devices thereof
patent, April 2014

CD69 and Regulatiof the Immune Function
journal, January 1999

Global quantitative phosphoprotein analysis using Multiplexed Proteomics technology
journal, July 2003

Single Cell Profiling of Circulating Tumor Cells: Transcriptional Heterogeneity and Diversity from Breast Cancer Cell Lines
journal, May 2012

LNA flow–FISH: A flow cytometry–fluorescence in situ hybridization method to detect messenger RNA using locked nucleic acid probes
journal, July 2009

Cytokine detection by antibody-based proximity ligation
journal, May 2004

Method for dialysis on microchips using thin porous polymer membrane
patent, May 2009

A custom microarray platform for analysis of microRNA gene expression
journal, September 2004

Direct observation of individual endogenous protein complexes in situ by proximity ligation
journal, October 2006

Rolling circle replication of padlock probes
patent, July 2006

CD69 Association with Jak3/Stat5 Proteins Regulates Th17 Cell Differentiation
journal, August 2010

Apparatus for DNA sequencing
patent, October 2001

Single-cell gene-expression profiling reveals qualitatively distinct CD8 T cells elicited by different gene-based vaccines
journal, March 2011

Sterile flow cytometer and sorter with mechanical isolation between flow chamber and sterile enclosure
patent, June 1997

The first analogues of LNA (Locked Nucleic Acids): Phosphorothioate-LNA and 2′-thio-LNA
journal, August 1998

A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA)
journal, March 2006

Fully Integrated Microfluidic Platform Enabling Automated Phosphoprofiling of Macrophage Response
journal, May 2009

Obtaining information from optical cavity output light
patent, March 2009

Miniaturized cytometer for detecting multiple species in a sample
patent-application, May 2005

Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes
journal, December 2004

Microchannel gel electrophoretic separation systems and methods for preparing and using
patent, February 2015

Microfluidically-unified cell culture, sample preparation, imaging and flow cytometry for measurement of cell signaling pathways with single cell resolution
journal, January 2012

Method for forming polymerized microfluidic devices
patent, November 2011

System for concentrating and analyzing particles suspended in a fluid
patent, April 2011

miRNA Detection at Single-Cell Resolution Using Microfluidic LNA Flow-FISH
book, January 2014

Isotropically etched radial micropore for cell concentration, immobilization, and picodroplet generation
journal, January 2009

Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs
journal, November 2005

Devices, systems, and methods for microscale isoelectric fractionation
patent, August 2016

Dielectrophoretic systems without embedded electrodes
patent, March 2006

Rolling circle replication of padlock probes
patent, May 2003

Foxp3-Dependent MicroRNA155 Confers Competitive Fitness to Regulatory T Cells by Targeting SOCS1 Protein
journal, January 2009

Method for voltage-gated protein fractionation
patent, April 2012

Microfluidic Molecular Assay Platform for the Detection of miRNAs, mRNAs, Proteins, and Posttranslational Modifications at Single-Cell Resolution
journal, December 2014

Devices, systems, and methods for microscale isoelectric fractionation
patent, April 2015

Dialysis membrane for separation on microchips
patent, July 2010

Microfluidic devices and methods including porous polymer monoliths
patent, April 2014

Microfluidic Platform For Cell Culture And Assay
patent-application, June 2011

Regulation of the Germinal Center Response by MicroRNA-155
journal, April 2007

Immuno-polymerase chain reaction system for antigen detection
patent, September 1997

Absolute quantitation of microRNAs with a PCR-based assay
journal, December 2006

Portable modular detection system
patent, October 2009

Method for forming polymerized microfluidic devices
patent, March 2013

Single-Cell Measurements of IgE-Mediated FcεRI Signaling Using an Integrated Microfluidic Platform
journal, March 2013

Microfluidic-Based Cell Sorting of Francisella tularensis Infected Macrophages Using Optical Forces
journal, August 2008

FISHing with locked nucleic acids (LNA): evaluation of different LNA/DNA mixmers
journal, August 2003

Microchannel gel electrophoretic separation systems and methods for preparing and using
patent, September 2013

Microfluidic device having an immobilized pH gradient and PAGE gels for protein separation and analysis
patent, December 2012

Dialysis on microchips using thin porous polymer membranes
patent, September 2007

Arrays, Substrates, Devices, Methods And Systems For Detecting Target Molecules
patent-application, February 2009

Single Cell MicroRNA Analysis Using Microfluidic Flow Cytometry
journal, January 2013

MicroRNA expression profiling of single whole embryonic stem cells
journal, January 2006

Rapid in situ codetection of noncoding RNAs and proteins in cells and formalin-fixed paraffin-embedded tissue sections without protease treatment
journal, May 2010

In Situ Proximity Ligation Assay for Microscopy and Flow Cytometry
journal, April 2011

Preconcentration and separation of analytes in microchannels
patent, November 2010

Ultrasensitive immunoassays
patent, April 2005

Systems, devices, and methods for agglutination assays using sedimentation
patent, January 2016

Sol-gel method for encapsulating molecules
patent, December 2002

Microwell cell-culture device and fabrication method
patent, September 2012

Bringing chemistry to life
journal, August 2011

Multi-analyte analysis of saliva biomarkers as predictors of periodontal and pre-implant disease
patent, April 2015

Multiplexed Proximity Ligation Assay
patent-application, July 2014

miRNA in situ hybridization in formaldehyde and EDC–fixed tissues
journal, January 2009

Apparatus and method for concentrating and filtering particles suspended in a fluid
patent, May 2009

Multidimensional electrophoresis and methods of making and using thereof
patent-application, June 2004