Multiplex spatial profiling of gene expression
The present invention provides mass tag complexes that permit simultaneously obtaining information of a plurality of biological molecules. The biological molecules may be RNA or protein, and the information includes both level of expression as well as spatial disposition within a cell or tissue. The mass tag comprise a core structure, a target binding structure (e.g., nucleic acid or peptide binding structure), a cleavable linker and a mass tag that exhibits a unique mass spectroscopy signal.
1. A mass tag complex comprising:
(i) a water-soluble core structure;
(ii) a target binding agent;
(iii) a mass unit that permits detection by mass spectroscopy; and
(iv) a cleavage site connected to said mass unit.
2. The complex of claim 1 , further comprising a spacer unit connected to said cleavage site and/or said target binding agent.
3. The complex of claim 1 , wherein said cleavage site is susceptible to photocleavage, chemical cleavage or enzymatic cleavage.
4. The complex of claim 1 , wherein said mass unit is a peptide.
5. The complex of claim 1 , wherein said target binding agent is an oligonucleotide that hybridizes to an RNA of interest.
6. The complex of claim 5 , wherein said oligonucleotide is about 8 to about 25 bases in length.
7. The complex of claim 1 , wherein said target binding agent is an antibody that binds to a protein of interest.
8. The complex of claim 7 , wherein said antibody is Ig, F(ab), F(ab′) 2 or single chain.
9. The complex of claim 1 , wherein said core structure is a polar-neutral, water-soluble structure.
10. The complex of claim 1 , wherein each of said target binding agent and said mass unit is independently linked to said core structure.
11. A population of mass tag complexes, each complex comprising:
(i) an identical core structure;
(ii) a target binding agent, wherein said population comprises a plurality of target binding agents with different target binding specificities;
(iii) a mass unit that permits detection by mass spectroscopy, wherein said population comprises a plurality of mass units that have different masses that can be differentiated by said mass spectroscopy; and
(iv) a cleavage site connected to said mass unit.
12. The population of claim 11 , wherein each complex further comprises a spacer unit connected to said each of cleavage sites and/or said target binding agents.
13. The population of claim 11 , wherein each of said mass units is a peptide.
14. The population of claim 11 , wherein each of said cleavage sites is photocleaved, enzymatically cleaved or chemically cleaved.
15. The population of claim 11 , wherein said each of said target binding agents is an oligonucleotide that hybridizes to a different RNA of interest.
16. The population of claim 15 , wherein each of said oligonucleotides is about 8 to about 25 bases in length.
17. The population of claim 11 , wherein each of said target binding agents is an antibody that binds to a different protein of interest.
18. The population of claim 17 , wherein each of said antibodies is Ig, F(ab), F(ab′) 2 or single chain.
19. The population of claim 11 , wherein each of said core structures is a polar-neutral, water-soluble structure.
20. The population of claim 11 , wherein each of said target binding agents and said mass units is independently linked to said core structure.
21. A method of simultaneously obtaining information on a plurality of distinct biomolecules comprising:
(a) providing a population of mass tag complexes, each complex comprising:
(i) an identical core structure;
(ii) a target binding agent, wherein said population comprises a plurality of binding agents with different target binding specificities;
(iii) a mass unit that permits detection by mass spectroscopy, wherein said population comprises a plurality of mass units that have different masses that can be differentiated by said mass spectroscopy; and
(iv) a cleavage site connected to said mass unit;
(b) contacting said population with a biomolecule-containing sample;
(c) cleaving said cleavage site; and
(d) subjecting said sample to mass spectroscopy.
22. The method of claim 21 , wherein said mass spectroscopy is MALDI-TOF.
23. The method of claim 21 , wherein cleavage site is photocleaved, and step (c) comprises subjecting said sample to an appropriate light source.
24. The method of claim 21 , further comprising the step, between steps (b) and (c), of spatially fixing said biomolecules and target binding agents.
25. The method of claim 24 , wherein said biomolecules and target binding agents are located in a cell.
26. The method of claim 25 , wherein said cell is from a patient with a pathologic condition.
27. The method of claim 26 , wherein said pathologic condition is cancer, an inflammatory disease, an infection, or a developmental disease.
28. The method of claim 25 , wherein said cell or patient has been treated with a therapy.
29. The method of claim 25 , wherein said cell is in comprised within an intact tissue specimen or an organism.
30. The method of claim 21 , wherein said mass unit is a peptide.
31. The method of claim 21 , wherein each of said target binding agents is an oligonucleotide that hybridizes to a different RNA of interest.
32. The method of claim 31 , wherein said oligonucleotide is about 8 to about 25 bases in length.
33. The method of claim 21 , wherein each of said target binding agents is an antibody that binds to a different protein of interest.
34. The method of claim 33 , wherein said antibody is Ig, F(ab), F(ab′) 2 or single chain.
35. The method of claim 21 , wherein said core structure is a polar-neutral, water-soluble structure.
36. A method of obtaining information on the spatial position of a biomolecule in a cell comprising:
(a) providing a mass tag complex comprising:
(i) a core structure;
(ii) a target binding agent;
(iii) a mass unit that permits detection by mass spectroscopy, wherein said population comprises a plurality of mass units that have different masses that can be differentiated by said mass spectroscopy; and
(iv) a cleavage site connected to said mass unit;
(b) contacting said mass tag complex with a cell-containing sample;
(c) spatially fixing said biomolecule and target binding agent;
(d) cleaving said cleavage site; and
(e) subjecting said sample to mass spectroscopy.
37. The method of claim 36 , further comprising obtaining information on the expression level of said biomolecule.
38. The method of claim 36 , further comprising obtaining information on a plurality of biomolecules by providing a population of mass tag complexes, each complex comprising an identical core structure; a target binding agent with a distinct target specificity; a distinct mass unit that permits detection by mass spectroscopy; and a cleavage site connected to said mass unit.
39. The method of claim 38 , wherein said biomolecule is an RNA or a protein.
40. The method of claim 36 , wherein said cell is located in an intact tissue specimen or an organism.