Methods, compositions, and devices for isolation and expression analysis of regions of interest from a tissue
Provided herein are structures and methods for isolating cellular components from at least one region of interest in a planar tissue section. Structures and methods as described can allow for isolation and tagging of tissue regions.
1. A method of isolating cellular components from at least one region of interest within a planar tissue section disposed onto a solid substrate, comprising:
(a) circumscribing at least one region of interest within the planar tissue section disposed onto the solid substrate by applying a chemical mask to the planar tissue section;
(b) solubilizing the cellular components within the at least one region of interest by dispensing a first solution comprising one or more extraction agents into the at least one region of interest whereby cells circumscribed within the at least one region of interest are selectively lysed, and a convex liquid dome is formed within each region of the at least one region of interest wherein the convex liquid dome is isolated from a fluid communication with other convex liquid domes in other regions of interest of the at least one region of interest and the other convex liquid domes are isolated from a fluid communication with each other.
2. The method of claim 1 , wherein the dispensing the first solution onto the region of interest comprises:
(a) dispensing the first solution into an agent transfer device comprising at least one agent transfer array element positioned on a surface of a second solid substrate;
(b) contacting the at least one agent transfer array element positioned on the surface of the second solid substrate with the planar tissue section, such that the at least one agent transfer array element spatially corresponds to the at least one region of interest in the planar tissue section, wherein the contacting enables a transfer of the first solution to the at least one region of interest in the planar tissue section.
3. The method of claim 1 , further comprising isolating at least one solubilized cellular component from the at least one region of interest within the planar tissue section on the solid substrate.
4. The method of claim 1 , further comprising sequencing nucleic acids among the at least one cellular component solubilized from the at least one region of interest.
5. The method of claim 1 , further comprising analyzing proteins among the at least one cellular component solubilized from the at least one region of interest using a tandem mass spectrometer.
6. The method of claim 1 , wherein the dispensing the first solution is performed with the first solution further comprising a soluble tag, wherein the soluble tag corresponds to the at least one region of interest.
7. The method of claim 6 , wherein the dispensing the first solution is performed with the first solution comprising the soluble tag being an oligonucleotide.
8. The method of claim 7 , wherein the dispensing the first solution is performed with the first solution comprising the oligonucleotide further comprising a sample index sequence corresponding to the region of interest and, optionally, a unique molecular identifier sequence.
9. The method of claim 7 , wherein the dispensing the first solution is performed with the first solution comprising the oligonucleotide comprising a charge tag corresponding to the region of interest.
10. The method of claim 7 , wherein the dispensing the first solution is performed with the first solution comprising the oligonucleotide being double-stranded.
11. The method of claim 7 , wherein the dispensing the first solution is performed with the first solution comprising the oligonucleotide being conjugated to a bead.
12. The method of claim 6 , wherein the dispensing the first solution is performed with the first solution comprising the soluble tag being a Tandem Mass Tag.
13. The method of claim 1 , wherein the dispensing the first solution is performed with the one or more extraction agents comprising surfactants, proteases, tonicity adjusting agents, chaotropes, nucleases, buffers, protease inhibitors, phosphatase inhibitors, or nuclease inhibitors or a combination thereof.
14. The method of claim 1 , wherein the applying the chemical mask is performed with the chemical mask having a contact angle between 60 degrees and 155 degrees.
15. The method of claim 1 , wherein the applying the chemical mask is performed using a hydrophobic mask solution comprising a fluoropolymer or a fluoroacrylic polymer.
16. The method of claim 15 , wherein the applying the chemical mask is performed using a second comprising an acrylate solution or cyano-acrylate solution.
17. The method of claim 16 , wherein the applying the chemical mask is performed with the chemical mask solution further comprising a solvent.
18. The method of claim 17 , wherein the applying the chemical mask is performed with chemical mask solution comprising the solvent being a propylene glycol derivative solvent, a fluorocarbon solvent, or an alcohol solvent.
19. The method of claim 17 , wherein the applying the chemical mask is performed with chemical mask solution comprising the solvent being a perfluorooctane solvent, a perfluoro-2-methylpentane solvent, a perfluoro-1,3-dimethylcyclohexane solvent, a perfluorodecalin solvent, or a 1,3-difluoropropane solvent.
20. The method of claim 1 , wherein each region of interest of the at least one region of interest is less than about 7.8×10 5 square microns in area.
21. The method of claim 2 , wherein the dispensing the first solution is performed with the at least one agent transfer array element positioned on the surface of the second solid substrate comprising at least one hydrophilic region circumscribed by a hydrophobic region.
22. The method of claim 1 , further comprising solubilizing cellular components from more than one region of interest in the planar tissue.
23. The method of claim 1 , wherein the applying the chemical mask is performed with the chemical mask circumscribing the at least one region of interest in the planar tissue section on the solid substrate being applied to the planar tissue section using a piezoelectric ink-jet delivery device.
24. The method of claim 1 , wherein the applying the chemical mask is performed with the planar tissue section being about 2 to about 50 μm in thickness.
25. The method of claim 1 , wherein the applying the chemical mask is performed with the planar tissue section being about 1 to about 15 μm in thickness.
26. The method of claim 1 , wherein the applying the chemical mask is performed with the planar tissue section being a formalin fixed, paraffin embedded (FFPE) tissue section.
27. The method of claim 1 , wherein the applying the chemical mask is performed with the planar tissue section being an unfixed tissue section.
28. The method of claim 1 , further comprising dispensing a second solution comprising one or more extraction agents onto the region of interest whereby a droplet containing liberated cellular components is formed, wherein the droplet is isolated from a fluid communication with a tissue outside the region of interest without the isolated droplet isolation being mediated by a solid physical barrier between the liberated cellular components and the tissue outside the region of interest.