System and Methods for Massively Parallel Analysis of Nucleic Acids in Single Cells

Abstract

Methods and systems are provided for massively parallel genetic analysis of single cells in emulsion droplets or reaction containers. Genetic loci of interest are targeted in a single cell using a set of probes, and a fusion complex is formed by molecular linkage and amplification techniques. Methods are provided for high-throughput, massively parallel analysis of the fusion complex in a single cell in a population of at least 10,000 cells. Also provided are methods for tracing genetic information back to a cell using barcode sequences.

1 . A method for analyzing at least two nucleic acid sequences in a single cell contained within a population of at least 10,000 cells, comprising:
 providing a first set of nucleic acid probes, the first set comprising a first probe comprising a sequence that is complementary to a first target nucleic acid subsequence, a second probe comprising a sequence that is complementary to a second subsequence of the first target nucleic acid and a second sequence that is complementary to an exogenous sequence, a third probe comprising the exogenous sequence and a sequence that is complementary to a first subsequence of a second target nucleic acid, and a fourth probe comprising a sequence that is complementary to a second subsequence of the second target nucleic acid sequence, wherein the first target nucleic acid or the second target nucleic acid comprises an endogenous sequence;   isolating the single cells with at least one set of nucleic acid probes;   amplifying the first and second target nucleic acid sequences independently, wherein the first target nucleic acid sequence is amplified using the first probe and the second probe, and wherein the second target nucleic acid sequence is amplified using the third probe and the fourth probe;   hybridizing the exogenous sequence to its complement;   amplifying the first target nucleic acid sequence, the second target nucleic acid sequence, and the exogenous sequence using the first and fourth probes, thereby generating a fused complex; and   performing a bulk sequencing reaction to generate sequence information for at least 100,000 fused complexes from at least 10,000 cells within the population of cells, wherein the sequence information is sufficient to co-localize the first target nucleic acid sequence and the second target nucleic acid sequence to a single cell from the population of at least 10,000 cells.   
     
     
         2 . The method of  claim 1 , wherein the single cell is isolated in an emulsion micro droplet. 
     
     
         3 . The method of  claim 1 , wherein the single cell is isolated in a reaction container. 
     
     
         4 . The method of  claim 1 , wherein the amplifying step comprises performing a polymerase chain reaction, and wherein the first and third probes are forward primers and the second and fourth probes are reverse primers for the polymerase chain reaction. 
     
     
         5 . The method of  claim 1 , wherein the amplifying step comprises performing a ligase chain reaction. 
     
     
         6 . The method of  claim 1 , wherein the amplifying step comprises performing a polymerase chain reaction, a reverse-transcriptase polymerase chain reaction, a ligase chain reaction, or a ligase chain reaction followed by a polymerase chain reaction. 
     
     
         7 . The method of  claim 1 , wherein the fused complex is circular. 
     
     
         8 . The method of  claim 1 , wherein the first or second target nucleic acid sequence is an RNA sequence. 
     
     
         9 . The method of  claim 1 , wherein the first or second target nucleic acid sequence is a DNA sequence. 
     
     
         10 . The method of  claim 1 , wherein the first or second target nucleic acid sequence comprises a T-cell receptor sequence. 
     
     
         11 . The method of  claim 1 , wherein the first target nucleic sequence, the second target nucleic acid sequence or both target nucleic acid sequences comprise an immunoglobulin sequence. 
     
     
         12 . The method of  claim 1 , wherein the first target nucleic acid comprises a T-cell receptor sequence, and the second target nucleic sequence comprises a second molecule that is associated with immune cell function. 
     
     
         13 . The method of  claim 12 , wherein the second molecule is selected from the group consisting of: interleukin-2 (IL-2), interleukin-4 (IL-4), interferon gamma (IFNγ), interleukin-10 (IL-10), interleukin-1 (IL-1), interleukin-13 (IL-13), interleukin-17 (IL-17), interleukin-18 (IL-18), tumor necrosis factor alpha (TNFα), tumor necrosis factor beta (TNFβ), T-box transcription factor 21 (TBX21), forkhead box P3 (FOXP3), cluster of differentiation 4 (CD4), cluster of differentiation 8 (CD8), cluster of differentiation 1d (CD1d), cluster of differentiation 161 (CD161), cluster of differentiation 3 (CD3), major histocompatibility complex (MHC), cluster of differentiation 19 (CD19), interleukin 7 receptor (IL-17 receptor), cluster of differentiation 10 (CD10), cluster of differentiation 20 (CD20), cluster of differentiation 22 (CD22), cluster of differentiation 34 (CD34), cluster of differentiation 27 (CD27), cluster of differentiation 5 (CD5), and cluster of differentiation 45 (CD45), cluster of differentiation 38 (CD38), cluster of differentiation 78 (CD78), interleukin-6 receptor, Interferon regulatory factor 4 (IRF4), and cluster of differentiation 138 (CD138). 
     
     
         14 . The method of  claim 1 , wherein the first target nucleic acid sequence comprises an immunoglobulin sequence, and the second sequence comprises a second molecule associated with immune cell function. 
     
     
         15 . The method of  claim 14 , wherein the second molecule is selected from the group consisting of: interleukin-2 (IL-2), interleukin-4 (IL-4), interferon gamma (IFNγ), interleukin-10 (IL-10), interleukin-1 (IL-1), interleukin-13 (IL-13), interleukin-17 (IL-17), interleukin-18 (IL-18), tumor necrosis factor alpha (TNFα), tumor necrosis factor beta (TNFβ), T-box transcription factor 21 (TBX21), forkhead box P3 (FOXP3), cluster of differentiation 4 (CD4), cluster of differentiation 8 (CD8), cluster of differentiation 1d (CD1d), cluster of differentiation 161 (CD161), cluster of differentiation 3 (CD3), major histocompatibility complex (MHC), cluster of differentiation 19 (CD19), interleukin 7 receptor (IL-17 receptor), cluster of differentiation 10 (CD10), cluster of differentiation 20 (CD20), cluster of differentiation 22 (CD22), cluster of differentiation 34 (CD34), cluster of differentiation 27 (CD27), cluster of differentiation 5 (CD5), and cluster of differentiation 45 (CD45), cluster of differentiation 38 (CD38), cluster of differentiation 78 (CD78), interleukin-6 receptor, Interferon regulatory factor 4 (IRF4), and cluster of differentiation 138 (CD138). 
     
     
         16 . The method of  claim 1 , wherein the first or second target nucleic acid comprises a rare gene sequence. 
     
     
         17 . The method of  claim 16 , wherein the rare gene sequence is present in fewer than 5% of the cells. 
     
     
         18 . The method of  claim 17 , wherein the rare gene sequence is present in fewer than 1% of the cells. 
     
     
         19 . The method of  claim 18 , wherein the rare gene sequence is present in fewer than 0.1% of the cells. 
     
     
         20 . The method of  claim 16 , wherein the rare gene sequence results from a genetic mutation. 
     
     
         21 . The method of  claim 20 , wherein the mutation is a somatic mutation. 
     
     
         22 . The method of  claim 20 , wherein the mutation is associated with a disease. 
     
     
         23 . The method of  claim 22 , wherein the disease is cancer. 
     
     
         24 . The method of  claim 20 , wherein the genetic mutation is a mutation in a gene selected from the group consisting of epidermal growth factor receptor (EGFR), phosphatase and tensin homolog (PTEN), tumor protein 53 (p53), MutS homolog 2 (MSH2), multiple endocrine neoplasia 1 (MEN1), adenomatous polyposis coli (APC), Fas receptor (FASR), retinoblastoma protein (Rb1), Janus kinase 2 (JAK2), (ETS)-like transcription factor 1 (ELK1), v-ets avian erythroblastosis virus E26 oncogene homolog 1 (ETS1), breast cancer 1 (BRCA1), breast cancer 2 (BRCA2), hepatocyte growth factor receptor (MET), ret protoco-oncogene (RET), V-erb-b2 erythroblastic leukemia viral oncogene homolog 2 (HER2), V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS), B-cell lymphoma 2 (BCL2), V-myc myelocytomatosis viral oncogene homolog (MYC), neurofibromatosis type 2 gene (NF2), v-myb myeloblastosis viral oncogene homolog (MYB), and mutS homolog 6 ( E. coli ) (MSH6). 
     
     
         25 . The method of  claim 23 , wherein the cancer is selected from the group consisting of: lung carcinoma, non-small cell lung cancer, small cell lung cancer, uterine cancer, thyroid cancer, breast carcinoma, prostate carcinoma, pancreas carcinoma, colon carcinoma, lymphoma, Burkitt lymphoma, Hodgkin lymphoma, myeloid leukemia, leukemia, sarcoma, blastoma, melanoma, seminoma, brain cancer, glioma, glioblastoma, cerebellar astrocytoma, cutaneous T-cell lymphoma, gastric cancer, liver cancer, ependymona, laryngeal cancer, neck cancer, stomach cancer, kidney cancer, pancreatic cancer, bladder cancer, esophageal cancer, testicular cancer, medulloblastoma, vaginal cancer, ovarian cancer, cervical cancer, basal cell carcinoma, pituitary adenoma, rhabdomyosarcoma, and Kaposi sarcoma. 
     
     
         26 . The method of  claim 1 , further comprising fixing and permeabilizing the cells prior to performing the amplification step. 
     
     
         27 . The method of  claim 1 , further comprising lysing the cells prior to performing the amplification step. 
     
     
         28 . The method of  claim 1 , further comprising quantifying the sequence information generated from the bulk sequencing reaction. 
     
     
         29 . The method of  claim 1 , wherein the single cell is contained within a population of at least 25,000 cells. 
     
     
         30 . The method of  claim 29 , wherein the single cell is contained within a population of at least 50,000 cells. 
     
     
         31 . The method of  claim 30 , wherein the single cell is contained within a population of at least 75,000 cells. 
     
     
         32 . The method of  claim 31 , wherein the single cell is contained within a population of at least 100,000 cells. 
     
     
         33 . The method of  claim 1 , wherein performing the bulk sequencing reaction to generate sequence information is carried out for at least 1,000,000 fused complexes from at least 10,000 cells within the population of cells. 
     
     
         34 . The method of  claim 1 , further comprising:
 providing a second set of nucleic acid probes, the second set comprising a fifth probe comprising a sequence that is complementary to a third target nucleic acid subsequence, a sixth probe comprising a sequence that is complementary to a second subsequence of the third target nucleic acid sequence and a second sequence that is complementary to a second exogenous sequence, a seventh probe comprising the exogenous sequence and a sequence that is complementary to a first subsequence of a fourth target nucleic acid sequence, and an eighth probe comprising a sequence that is complementary to a second subsequence of the fourth target nucleic acid sequence;   isolating the single cells with the first and second sets of nucleic acid probes;   amplifying the third and fourth target nucleic acid sequences independently, wherein the third target nucleic acid sequence is amplified using the fifth probe and the sixth probe, and wherein the fourth target nucleic acid sequence is amplified using the seventh probe and the eighth probe;   hybridizing the exogenous sequence to its complement;   amplifying the third target nucleic acid sequence, the fourth target nucleic acid sequence and the exogenous sequence using the fifth and eighth probes, thereby generating a fused complex; and   performing a bulk sequencing reaction to generate sequence information for at least 100,000 fused complexes from at least 10,000 cells within the population of cells, wherein the sequence information is sufficient to co-localize the first target nucleic acid sequence, the second target nucleic acid sequence, the third target nucleic acid sequence, and the fourth target nucleic acid sequence to a single cell from the population of at least 10,000 cells.   
     
     
         35 . The method of  claim 34 , wherein the first target nucleic acid sequence and the third target nucleic acid sequence are the same. 
     
     
         36 . The method of  claim 34 , wherein the first target nucleic acid sequence and the third target nucleic acid sequence are different. 
     
     
         37 . The method of  claim 1 , further comprising:
 providing N sets of nucleic acid probes, wherein each of the N sets comprise an I 1  probe comprising a sequence that is complementary to an I a  target nucleic acid first subsequence, an I 2  probe comprising a sequence that is complementary to an I a  target nucleic acid second subsequence and a second sequence that is complementary to an I exogenous sequence, an I 3  probe comprising the I exogenous sequence and a sequence that is complementary to an I b  target nucleic acid first subsequence, and an I 4  probe comprising a sequence that is complementary to an h target nucleic acid second subsequence, wherein I ranges from 1 to N;   isolating the single cells with the N sets of nucleic acid probes;   amplifying for all values of I, the I a  and I b  target nucleic acid sequences independently, wherein the I a  target nucleic acid sequence is amplified using the I 1  probe and the I 2  probe and the I b  target nucleic acid sequence is amplified using the I 3  probe and the I 4  probe;   hybridizing the I exogenous sequence to its complement;   amplifying for each I, the I a  target sequence, the I b  target sequence and the I exogenous sequence using the I 1  and I 4  probes, thereby generating N fused complexes; and   performing a bulk sequencing reaction to generate sequence information for at least 100,000 fused complexes from at least 10,000 cells within the population of cells, wherein the sequence information is sufficient to co-localize the N I a  target nucleic acid sequence and the I b  target nucleic acid sequence to a single cell from the population of at least 10,000 cells.   
     
     
         38 . The method of  claim 37 , wherein N is less than or equal to 10. 
     
     
         39 . The method of  claim 37 , wherein N is less than or equal to 100. 
     
     
         40 . The method of  claim 37 , wherein N is less than or equal to 1000. 
     
     
         41 . The method of  claim 37 , wherein N is less than or equal to 10,000. 
     
     
         42 . The method of  claim 37 , wherein N is less than or equal to 100,000. 
     
     
         43 . The method of  claim 37 , wherein N represents all of the polyadenylated transcripts in a cell. 
     
     
         44 . A method for analyzing at least two nucleic acid sequences in a single cell contained within a population of at least 10,000 cells, comprising:
 isolating each of a plurality of single cells from a population of at least 10,000 cells in an emulsion microdroplet or a reaction container,   introducing a unique barcode sequence comprising at least six nucleotides into each of the plurality of single cells, wherein each barcode sequence is selected from a pool of barcode sequences with greater than 1000-fold diversity in sequence;   for each of the plurality of single cells,
 providing at least one set of nucleic acid probes, the set comprising a first probe comprising a sequence that is complementary to a nucleic acid sequence that is located at the 5′ end of the barcode sequence, a second probe comprising a sequence that is complementary to a nucleic acid sequence that is located at the 3′ end of the barcode sequence and a second region of sequence that is complementary to a non-human, exogenous sequence, a third probe comprising a sequence that comprises the non-human, exogenous sequence and a sequence that is complementary to a first subsequence of a second target nucleic acid sequence, and a fourth probe comprising a sequence that is complementary to a second subsequence of the second target nucleic acid sequence, and wherein the second target nucleic acid sequence comprises an endogenous sequence; 
 amplifying the first and second nucleic acid sequences independently, wherein the first target nucleic acid sequence is amplified using the first probe and the second probe, and wherein the second target nucleic acid sequence is amplified using the third probe and the fourth probe; 
 hybridizing the exogenous sequence to its complement; 
 amplifying the first target nucleic acid sequence, the second target nucleic acid sequence, and the exogenous sequence using the first and fourth probes; 
   performing bulk sequencing of the fused complexes; and   identifying a single cell for each of the fused complexes based on the barcode sequence.   
     
     
         45 . The method of  claim 44 , wherein the barcode sequence is affixed to a bead or a solid surface. 
     
     
         46 . The method of  claim 45 , wherein the bead or the solid surface is isolated in the emulsion microdroplet or the reaction container. 
     
     
         47 . The method of  claim 46 , wherein introducing a unique barcode sequence comprises fusing the emulsion microdroplet or a reaction container comprising the single cell with the emulsion microdroplet or a reaction container comprising the barcode sequence affixed to the bead or the solid surface. 
     
     
         48 . The method of  claim 44 , wherein the second target nucleic acid sequence is complementary to an RNA sequence. 
     
     
         49 . The method of  claim 44 , wherein the second target nucleic acid sequence is complementary to a DNA sequence. 
     
     
         50 . The method of  claim 44 , wherein amplifying comprises performing a polymerase chain reaction. 
     
     
         51 . The method of  claim 44 , wherein amplifying comprises performing a ligase chain reaction. 
     
     
         52 . The method of  claim 44 , wherein amplifying comprises performing by ligase chain reaction followed by polymerase chain reaction. 
     
     
         53 . The method of  claim 44 , wherein the single cell is contained within a population of at least 25,000 cells. 
     
     
         54 . The method of  claim 53 , wherein the single cell is contained within a population of at least 50,000 cells. 
     
     
         55 . The method of  claim 54 , wherein the single cell is contained within a population of at least 75,000 cells. 
     
     
         56 . The method of  claim 55 , wherein the single cell is contained within a population of at least 100,000 cells. 
     
     
         57 . The method of  claim 44 , further comprising quantifying the fused complexes. 
     
     
         58 . The method of  claim 44 , wherein the fused complexes are circular. 
     
     
         59 . The method of  claim 44 , further comprising:
 providing N sets of nucleic acid probes, wherein each of the N sets comprise an I 1  probe comprising a sequence that is complementary a first subsequence of a barcode sequence, an I 2  probe comprising a sequence that is complementary to a second subsequence of the barcode sequence and a second sequence that is complementary to an I exogenous sequence, an I 3  probe comprising the I exogenous sequence and a sequence that is complementary to an I b  target nucleic acid first subsequence, and an I 4  probe comprising a sequence that is complementary to an h target nucleic acid second subsequence, wherein I ranges from 1 to N;   isolating the single cells with the N sets of nucleic acid probes;   amplifying for all values of I, the barcode sequence and the I b  target nucleic acid sequences independently, wherein the barcode sequence is amplified using the I 1  probe and the I 2  probe and the I b  target nucleic acid sequence is amplified using the I 3  probe and the I 4  probe;   hybridizing the I exogenous sequence to its complement;   amplifying for each I, the barcode sequence, the I b  target sequence and the I exogenous sequence using the I 1  and I 4  probes, thereby generating N fused complexes; and   performing a bulk sequencing reaction to generate sequence information for at least 100,000 fused complexes from at least 10,000 cells within the population of cells, wherein the sequence information is sufficient to co-localize the barcode sequence and the h target nucleic acid sequence to a single cell from the population of at least 10,000 cells.   
     
     
         60 . The method of  claim 59 , wherein N is less than or equal to 10. 
     
     
         61 . The method of  claim 59 , wherein N is less than or equal to 100. 
     
     
         62 . The method of  claim 59 , wherein N is less than or equal to 1000. 
     
     
         63 . The method of  claim 59 , wherein N is less than or equal to 10,000. 
     
     
         64 . The method of  claim 59 , wherein N is less than or equal to 100,000. 
     
     
         65 . The method of  claim 59 , wherein N represents all of the polyadenylated transcripts in a cell. 
     
     
         66 . The method of  claim 59 , wherein the barcode sequence is the same sequence for all N. 
     
     
         67 . A method for introducing unique barcode sequences into reaction containers or emulsion microdroplets, comprising:
 providing a pool of unique barcode sequences, wherein each barcode sequence is linked to a selection resistance gene;   providing a population of single cells;   transfecting the population of single cells with the pool of unique barcode sequences;   selecting cells comprising a unique barcode sequence, an endogenous target nucleic acid sequence, and the selection resistance gene; and   isolating each of the selected cells into reaction containers or emulsion microdroplets.   
     
     
         68 . The method of  claim 67 , wherein the selection resistance gene comprises a gene that encodes resistance to gentamycin, neomycin, hygromycin, or puromycin.