Methods and systems for determining spatial patterns of biological targets in a sample
The present disclosure provides methods and assay systems for use in spatially encoded biological assays, including assays to determine a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample. In particular, the biological targets comprise proteins, and the methods and assay systems do not depend on imaging techniques for the spatial information of the targets. The present disclosure provides methods and assay systems capable of high levels of multiplexing where reagents are provided to a biological sample in order to address tag the sites to which reagents are delivered; instrumentation capable of controlled delivery of reagents; and a decoding scheme providing a readout that is digital in nature.
1. A system for determining the presence and/or location of a target protein in a sample, the system comprising:
(a) a plurality of first probes, wherein a first probe of the plurality of first probes comprises: (i) a binding moiety that specifically binds to the target protein, and (ii) an oligonucleotide conjugated to the binding moiety;
(b) a plurality of second probes, wherein a second probe of the plurality of second probes comprises: (i) a sequence substantially complementary to a portion of the oligonucleotide of step (a), (ii) a first address tag that identifies a first area in the sample, and (iii) a first ligation region;
(c) a plurality of third probes, wherein a third probe of the plurality of third probes comprises: (i) a second address tag that identifies a second area in the sample, and (ii) a second ligation region;
(d) a first microfluidic device comprising multiple first addressing channels, wherein the second probe is delivered through a first addressing channel of the multiple first addressing channels; and
(e) a second microfluidic device comprising multiple second addressing channels, wherein the third probe is delivered through a second addressing channel of the multiple second addressing channels.
2. The system of claim 1 , wherein the multiple first addressing channels are substantially parallel to each other and the multiple second addressing channels are substantially parallel to each other.
3. The system of claim 1 , wherein the multiple first addressing channels and/or the multiple second addressing channels is n addressing channels, wherein n is an integer between 20 and 1000.
4. The system of claim 1 , wherein the width of each of the multiple first addressing channels and/or each of the multiple second addressing channels is about 1 μm to about 500 μm.
5. The system of claim 1 , wherein the depth of each of the multiple first addressing channels and/or each of the multiple second addressing channels is about 1 μm to about 500 μm.
6. The system of claim 1 , wherein the distance between each of the multiple first addressing channels and/or between each of the multiple second addressing channels is about 1 μm to about 2.0 mm.
7. The system of claim 1 , wherein the second area forms an angle with the first area at an intersection between the first area and the second area, and wherein the angle is about 10 degrees to about 90 degrees.
8. The system of claim 1 , wherein the third probe further comprises a variable tag region, a primer sequence, a sequencing adaptor, a biotin moiety, or a combination thereof.
9. The system of claim 1 , further comprising a splint oligonucleotide, wherein the splint oligonucleotide is substantially complementary to all or a portion of the first ligation region and all or a portion of the second ligation region.
10. The system of claim 1 , wherein the binding moiety comprises an antibody or an antigen binding fragment thereof, an aptamer, a small molecule, an affinity capture agent, or a combination thereof.
11. The system of claim 1 , wherein the sample is a freshly isolated tissue sample, a fixed tissue sample, a frozen tissue sample, an embedded tissue sample, a processed tissue sample, or a combination thereof.
12. The system of claim 1 , further comprising one or more enzymes selected from a polymerase, a reverse transcriptase, or a ligase.
13. The system of claim 1 , further comprising a module for imaging the sample.
14. The system of claim 1 , wherein the system further determines the presence and/or location of a target polynucleotide, and wherein the sequence substantially complementary to a portion of the oligonucleotide of step (a) is substantially complementary to at least a portion of the target polynucleotide.
15. The system of claim 14 , wherein the target polynucleotide is an RNA molecule.
16. The system of claim 15 , wherein the RNA molecule is an mRNA molecule.
17. The system of claim 14 , wherein the portion of the target polynucleotide is a poly(A) sequence.
18. A system for determining the presence or location of a target polynucleotide in a sample, the system comprising:
(a) a plurality of first probes, wherein a first probe of the plurality of first probes comprises: (i) a sequence substantially complementary to at least a portion of the target polynucleotide, (ii) a first address tag that identifies a first area in the sample, and (iii) a first ligation region;
(b) a plurality of second probes, wherein a second probe of the plurality of second probes comprises: (i) a second address tag that identifies a second area in the sample and (ii) a second ligation region;
(c) a first microfluidic device comprising multiple first addressing channels, wherein the first probe is delivered through a first addressing channel of the multiple first addressing channels to the first area; and
(d) a second microfluidic device comprising multiple second addressing channels, wherein the second probe is delivered through a second addressing channel of the multiple second addressing channels to the second area.
19. The system of claim 18 , wherein the multiple first addressing channels are substantially parallel to each other and the multiple second addressing channels are substantially parallel to each other.
20. The system of claim 18 , wherein the multiple first addressing channels and/or the multiple second addressing channels is n addressing channels, wherein n is an integer between 20 and 1000.
21. The system of claim 18 , wherein the width of each of the multiple first addressing channels and/or each of the multiple second addressing channels is about 1 μm to about 500 μm.
22. The system of claim 18 , wherein the depth of each of the multiple first addressing channels and/or each of the multiple second addressing channels is about 1 μm to about 500 μm.
23. The system of claim 18 , wherein the distance between each of the multiple first addressing channels and/or between each of the multiple second addressing channels is about 1 μm to about 2.0 mm.
24. The system of claim 18 , wherein the second area forms an angle with the first area at an intersection between the first area and the second area, and wherein the angle is about 10 degrees to about 90 degrees.
25. The system of claim 18 , wherein the second probe further comprises a variable tag region, a primer sequence, a sequencing adaptor, a biotin moiety, or a combination thereof.
26. The system of claim 18 , further comprising a splint oligonucleotide, wherein the splint oligonucleotide is substantially complementary to all or a portion of the first ligation region and all or a portion of the second ligation region.
27. The system of claim 18 , wherein the target polynucleotide is an mRNA molecule.
28. The system of claim 18 , wherein the sample is a freshly isolated tissue sample, a fixed tissue sample, a frozen tissue sample, an embedded tissue sample, a processed tissue sample, or a combination thereof.
29. The system of claim 18 , further comprising one or more enzymes selected from a polymerase, a reverse transcriptase, or a ligase.
30. The system of claim 18 , further comprising a module for imaging the sample.