Devices and methods for analyzing biological samples

Abstract

Described herein are systems and methods for analyzing biological samples. Including a method for processing an analyte, comprising providing a fluidic device comprising the analyte and one or more polymer precursors; selecting a discrete area within said fluidic device; providing an energy source in optical communication with fluidic device; and selectively supplying a unit of energy generated from the energy source to the fluidic device to generate a polymer matrix within the fluidic device, wherein the polymer matrix is within the discrete area or adjacent to the discrete area.

What is claimed is: 
     
         1 . A method of analyzing one or more biological components of a biological sample, the method comprising:
 providing a fluidic device comprising (i) a channel comprising a first surface, a biological sample, and one or more polymer precursors, wherein one or more biological components of the biological sample are disposed on or adjacent to the first surface, (ii) a spatial energy modulating element in optical communication with the first surface, and (iii) a detector that identifies positions of the one or more biological components in the channel based on one or more optical signals therefrom; and   synthesizing one or more chambers in the channel enclosing each of the one or more biological components by projecting light into the channel with the spatial energy modulating element such that the projected light causes cross-linking of the one or more polymer precursors to form polymer matrix walls of the chambers, wherein the position of each of the synthesized chambers is determined by the position of a biological component enclosed thereby identified by the detector.   
     
     
         2 . The method of  claim 1  wherein said biological sample comprises one or more cells and wherein said first surface comprises one or more capture elements for capturing one or more biological components of said biological sample. 
     
     
         3 . The method of  claim 2  wherein said one or more cells comprise one or more mammalian cells. 
     
     
         4 . The method of  claim 2  further comprising loading into said channel a lysing reagent so that said one or more cells in said chambers are lysed and said biological components of said one or more cells is released and captured by said capture elements. 
     
     
         5 . The method of  claim 4  wherein said biological components comprise intracellular proteins. 
     
     
         6 . The method of  claim 4  wherein said biological components comprise RNA or DNA and wherein said capture elements comprise capture oligonucleotides that capture such RNA or DNA. 
     
     
         7 . The method of  claim 6  wherein said RNA comprises messenger RNA. 
     
     
         8 . The method of  claim 7  further comprising depolymerizing said polymer matrix walls of said chambers and loading said channel with reverse transcriptase reagents to copy said captured messenger RNAs to produce complementary DNAs. 
     
     
         9 . The method of  claim 8  further comprising: (a) amplifying said complementary DNAs, (b) sequencing the amplified complementary DNAs, and (c) determining a transcriptome of each of said cells of each of said chambers. 
     
     
         10 . The method of  claim 9  wherein said amplifying comprises bridge amplifying each of said complementary DNAs to form a cluster for each thereof and wherein said sequencing comprises sequencing by synthesis said complementary DNA of each cluster. 
     
     
         11 . The method of  claim 4  wherein (i) said capture elements comprise barcodes each of which indicate a position thereof on said first surface, (ii) said biological components comprise RNA or DNA, and (iii) said capture elements comprise capture oligonucleotides that capture such RNA or DNA. 
     
     
         12 . The method of  claim 11  wherein said RNA comprises messenger RNA and further comprising depolymerizing said polymer matrix walls of said chambers and loading said channel with reverse transcriptase reagents to copy the captured messenger RNAs to produce complementary DNAs. 
     
     
         13 . The method of  claim 12  further comprising: (a) sequencing the complementary DNAs, and (b) determining a transcriptome of each of said cells of each of said chambers from the sequences of the complementary DNAs. 
     
     
         14 . The method of  claim 13  wherein each of said barcodes further comprises a universal molecular identifier. 
     
     
         15 . The method of  claim 2  wherein said capture elements comprise barcodes indicating a position thereof on said first surface and further comprising (i) incubating said one or more cells with antibodies specific for surface proteins whose relative expression permits identification of said cells, wherein each of such antibodies has an oligonucleotide label comprising an antibody-specific barcode capable of being captured by said capture element; and (ii) after said synthesizing, loading into said channel a lysing reagent so that said one or more cells in said chambers are lysed, so that oligonucleotide labels of antibodies attached to said one or more cells are released and captured by said capture elements. 
     
     
         16 . The method of  claim 15  further comprising depolymerizing said polymer matrix walls of said chambers and loading said channel with reagents to copy said captured oligonucleotide labels and said barcode of said capture element to produce complementary DNAs each with said barcode indicating position on said first surface. 
     
     
         17 . The method of  claim 16  further comprising: (a) amplifying said complementary DNAs and barcodes (b) sequencing the amplified complementary DNAs and barcodes, and (c) determining relative expression of said surface proteins for each of said cells of each of said chambers. 
     
     
         18 . The method of  claim 17  wherein said antibodies are selected to identify said one or more cells as CD8+ T cells, monocytes, CD4+ T cells, NK cells, DC cells and B cells. 
     
     
         19 . The method of  claim 1  (i) wherein said biological sample comprises one or more cells secreting proteins, (ii) further comprising combining therewith protein-capture beads comprising protein-capture antibodies; (iii) wherein said synthesizing further includes enclosing each of the one or more cells with one or more protein-capture beads adjacent thereto; and (iv) further comprising, after said synthesizing, (A) incubating the one or more cells secreting proteins with the protein-capture beads so that secreted proteins are captured by adjacent protein-capture beads; and (B) loading labeled protein detection antibodies and detecting protein secreted by each of the one or more cells by an amount of labeled protein detection antibodies on protein-capture beads adjacent to each of the one or more cells. 
     
     
         20 . The method of  claim 1  wherein said polymer matrix walls are degradable by treating with a degradation agent and wherein said method further comprises:
 identifying one or more of said chambers comprising said biological components that have selected characteristics based on said one or more optical signals; and 
 degrading said polymer matrix walls of the identified one or more said chambers based on the selected characteristics. 
 
     
     
         21 . The method of  claim 20  wherein said polymer matrix walls comprise photocleavable crosslinkers cleavable by exposure to light of a different wavelength than that of said wavelength of light used to synthesize said polymer matrix walls. 
     
     
         22 . The method of  claim 20  wherein said polymer matrix walls comprise acid labile crosslinkers and a photoacid generators and wherein said degrading comprises selectively directing a beam of light to said identified one or more chambers to stimulate the photoacid generators therein to generate acid to cleave the acid labile crosslinkers. 
     
     
         23 . The method of  claim 20  wherein said polymer matrix walls comprise base labile crosslinkers and photobase generators and wherein said degrading comprises selectively directing a beam of light to said identified one or more chambers to stimulate the photobase generators therein to generate basic conditions to cleave the base labile crosslinkers. 
     
     
         24 . The method of  claim 1  wherein said polymer matrix walls are degradable by treating with a degradation agent and wherein said method further comprises:
 identifying one or more of said chambers comprising said biological components that have selected characteristics based on said one or more optical signals; 
 loading said channel with a second reaction mixture comprising second polymer precursors, wherein the second polymer precursors are capable of forming second polymer matrix walls which are nondegradable for at least one degradation agent; and 
 synthesizing second chambers enclosing the identified chambers. 
 
     
     
         25 . The method of  claim 24  further comprising degrading said chambers, thereby separating said biological components comprising said selected characteristics. 
     
     
         26 . The method of  claim 1  wherein said channel comprises an optically transmissive material. 
     
     
         27 . The method of  claim 1  wherein said spatial energy modulating element is a digital micromirror device. 
     
     
         28 . The method of  claim 1  wherein said biological components are disposed randomly on said first surface. 
     
     
         29 . The method of  claim 1  wherein said channel of said fluidic device further comprises a second surface wherein said first surface and the second surface are disposed opposite one another across said channel, and wherein said polymer matrix walls of said chambers extend from said first surface to the second surface to form one or more chambers each comprising an interior. 
     
     
         30 . The method of  claim 29  wherein said interiors of a portion of said one or more chambers each contains a biological component.