Method and product for localized or spatial detection of nucleic acid in a tissue sample
The present invention relates to methods and products for the localized or spatial detection of nucleic acid in a tissue sample and in particular to a method for localized detection of nucleic acid in a tissue sample comprising: (a) providing an array comprising a substrate on which multiple species of capture probes are directly or indirectly immobilized such that each species occupies a distinct position on the array and is oriented to have a free 3′ end to enable said probe to function as a primer for a primer extension or ligation reaction, wherein each species of said capture probe comprises a nucleic acid molecule with 5′ to 3′: (i) a positional domain that corresponds to the position of the capture probe on the array, and (ii) a capture domain; (b) contacting said array with a tissue sample such that the position of a capture probe on the array may be correlated with a position in the tissue sample and allowing nucleic acid of the tissue sample to hybridize to the capture domain in said capture probes; (c) generating DNA molecules from the captured nucleic acid molecules using said capture probes as extension or ligation primers, wherein said extended or ligated DNA molecules are tagged by virtue of the positional domain; (d) optionally generating a complementary strand of said tagged DNA and/or optionally amplifying said tagged DNA; (e) releasing at least part of the tagged DNA molecules and/or their complements or amplicons from the surface of the array, wherein said part includes the positional domain or a complement thereof; and (f) directly or indirectly analyzing the sequence of the released DNA molecules.
1. A method for localized detection of mRNA in a tissue sample comprising cells, said method comprising:
(a) providing an array comprising a plurality of features on a substrate, each feature comprising a different capture probe directly immobilized thereon such that the capture probe has a free 3′ end, each feature occupying a distinct position on the array and having an area of less than about 1 mm 2 , each capture probe consisting of a nucleic acid molecule comprising the following domains oriented 5′ to 3′:
(i) a cleavage domain comprising a nucleotide sequence that is recognized by one or more enzymes capable of cleaving a nucleic acid molecule;
(ii) a positional domain comprising a nucleotide sequence unique to a particular feature; and
(iii) a capture domain comprising a nucleotide sequence that is designed for the selective capture of mRNA;
(b) contacting said array with the tissue sample comprising cells such that the tissue sample contacts a plurality of the features at their distinct positions on the array;
(c) hybridizing the mRNA present in the tissue sample comprising cells that are complementary to the capture sequences of the capture probes immobilized on the features, such that the mRNA is captured by the capture domain of the capture probes in the features;
(d) generating cDNA molecules from the captured mRNA, by extending the capture probes enzymatically using the captured mRNA as an extension template, such that the cDNA molecules comprise the nucleotide sequences or sequences of the positional domains;
(e) releasing at least part of the cDNA molecules from the features of the surface of the array with a cleavage enzyme that recognizes a nucleotide sequence in the cleavage domain and cleaves the cDNA molecules at a position that is 5′ to the positional domain;
(f) amplifying the cDNA molecules released in step (e); and
(g) identifying nucleotide sequences of the positional domain or sequences complementary to the nucleotide sequences of the positional domain present in the released amplified cDNA molecules, wherein the presence of the nucleotide sequence of the positional domain unique to a given particular feature or the sequence complementary to the nucleotide sequence of the positional domain unique to said particular feature indicates that the released amplified cDNA molecule was obtained from mRNA present in the tissue sample comprising cells at the distinct position where the tissue sample comprising cells contacted said particular feature.
2. The method of claim 1 , wherein the capture domain that is designed for the selective capture of mRNA hybridizes to the poly-A tail of mRNA.
3. The method of claim 1 , wherein the domain that is designed for the selective capture of mRNA comprises a poly-T sequence.
4. The method of claim 1 , wherein step (g) comprises sequencing the released amplified cDNA molecules.
5. The method of claim 1 further comprising a step of generating a complementary strand of the cDNA molecules prior to amplifying said cDNA molecules.
6. The method of claim 1 , further comprising determining which genes are expressed at a particular distinct location of the tissue sample comprising cells by a method comprising determining the sequences of the released amplified cDNA molecules comprising the same nucleotide sequence of a positional domain or sequence complementary the nucleotide sequence of a positional domain.
7. The method of claim 1 , further comprising correlating the nucleotide sequence of a positional domain unique to a given particular feature or the sequence complementary to the nucleotide sequence of a positional domain unique to said particular feature present in the released amplified cDNA molecules to a position in the tissue sample.
8. The method of claim 7 , comprising correlating the nucleotide sequence of a positional domain unique to a given particular feature or the sequence complementary to the nucleotide sequence of a positional domain unique to said particular feature present in the released amplified cDNA molecules to an image of the tissue sample.
9. The method of claim 1 , wherein the tissue sample comprising cells is a tissue section.
10. The method of claim 1 , wherein the tissue sample comprising cells is a cell suspension.
11. The method of claim 1 , wherein capture probes are immobilized on the substrate by a chemical linker.
12. The method of claim 1 , wherein the array comprises at least 10 features.
13. The method of claim 1 , wherein the array comprises at least 50 features.
14. The method of claim 1 , wherein the array comprises at least 100 features.
15. The method of claim 1 , wherein the array is a bead array and the capture probes are immobilized directly on the beads of the array.
16. The method of claim 1 , wherein the step of generating cDNA molecules from the captured mRNA, comprises extending the capture probes with a reverse transcriptase enzyme using the captured mRNA as an extension template.