Tissue preservation and fixation method
This invention relates, e.g., to a composition that, at room temperature, when contacted with a sample comprising phosphoproteins, can fix and stabilize cellular phosphoproteins, preserve cellular morphology, and allow the sample to be frozen to generate a cryostat frozen section suitable for molecular analysis. The composition comprises (1) a fixative that is effective to fix the phosphoproteins, and that has a sufficient water content to be soluble for a stabilizer and/or a permeability enhancing agent); (2) a stabilizer, comprising (a) a kinase inhibitor and (b) a phosphatase inhibitor and, optionally, (c) a protease (e.g., proteinase) inhibitor; and (3) a permeability enhancing agent (e.g. PEG). Methods are described for preserving phosphoproteins, using such a composition. Also described are endogenous surrogate markers for monitoring protein degradation, including the loss of posttranslational modifications (such as phosphorylation), e.g. the following removal of a cell or tissue from a subject; and exogenous molecular sentinels (e.g. phosphoproteins attached to magnetic nanoparticles) that allow one to evaluate the processing history of a cellular or tissue population sample.
1. A composition for preserving a sample comprising proteins, said composition comprising:
a. a fixative that stabilizes the proteins in the sample and that has a sufficient water content for a stabilizer and/or a permeability enhancing agent to be soluble therein;
b. a stabilizer, comprising (i) a kinase inhibitor and (ii) a phosphatase inhibitor, and, optionally, (iii) a protease inhibitor; and
c. a permeability enhancing agent,
wherein the proteins are phosphoproteins and wherein the fixative comprises methanol or ethanol, the kinase inhibitor comprises staurosporine or genistein, the phosphatase inhibitor comprises sodium orthovanadate or beta glycerophosphate, and the permeability enhancing agent comprises water, dimethylsulfoxide, or polyethylene glycol.
2. The composition of claim 1 , wherein the fixative comprises a particulate material comprising bioceramic, poly diol citrate, chitosan, or hydroxyapatite; a chelation agent; trichloroacetic acid (TCA); chloroform or methanol; or ammonium sulfate.
3. The composition of claim 1 , wherein the permeability enhancing agent comprises a polymer or a nanoparticle.
4. The composition of claim 1 , further comprising one or more cross-linking agents.
5. The composition of claim 4 , wherein the fixative comprises ethanol, the kinase inhibitor comprises staurosporine and genistein, the phosphatase inhibitor comprises sodium orthovanadate and beta glycerophosphate, the permeability enhancing agent comprises polyethylene glycol, and the cross-linking agent comprises dithiobis-succinimidylpropionate.
6. The composition of claim 1 , wherein the stabilizer is attached to the permeability enhancing agent.
7. The composition of claim 1 , wherein the stabilizer and the permeability enhancing agent are attached to a nanoparticle.
8. A kit for fixing proteins in a sample, comprising the components of the composition of claim 1 and a sentinel comprising a particulate entity attached to one or more surrogate phosphoprotein markers, in one or more containers.
9. A method for preserving proteins in a sample, comprising contacting the sample with the composition of claim 1 , under conditions effective for the preservation of proteins in the sample.
10. The method of claim 9 , further comprising analyzing the phosphorylation state of at least one phosphoprotein in the sample.
11. The composition of claim 4 wherein the one or more crosslinking agents comprises dithiobis-succinimidylpropionate.
12. A composition for preserving a sample comprising proteins, said composition comprising:
a. a fixative that stabilizes the proteins in the sample and that has a sufficient water content for a stabilizer and/or a permeability enhancing agent to be soluble therein;
b. a stabilizer, comprising (i) a kinase inhibitor and (ii) a phosphatase inhibitor;
c. a permeability enhancing agent; and
d. a cross-linking agent.
13. The composition of claim 12 wherein the stabilizer further comprises a protease inhibitor.
14. The composition of claim 12 wherein the proteins are phosphoproteins and wherein the fixative comprises methanol or ethanol, the kinase inhibitor comprises staurosporine or genistein, the phosphatase inhibitor comprises sodium orthovanadate or beta glycerophosphate, and the permeability enhancing agent comprises water, dimethylsulfoxide, or polyethylene glycol.
15. The composition of claim 12 , wherein the proteins are phosphoproteins and wherein the fixative comprises ethanol, the kinase inhibitor comprises staurosporine and genistein, the phosphatase inhibitor comprises sodium orthovanadate and beta glycerophosphate, the permeability enhancing agent comprises polyethylene glycol, and the cross-linking agent comprises dithiobis-succinimidylpropionate.
16. The composition of claim 13 , wherein the proteins are phosphoproteins and wherein the fixative comprises ethanol, the kinase inhibitor comprises staurosporine and genistein, the phosphatase inhibitor comprises sodium orthovanadate and beta glycerophosphate, the permeability enhancing agent comprises polyethylene glycol, and the cross-linking agent comprises dithiobis-succinimidylpropionate.
17. The composition of claim 12 , wherein the fixative comprises a particulate material comprising bioceramic, poly diol citrate, chitosan, or hydroxyapatite; a chelation agent; trichloroacetic acid (TCA); chloroform or methanol; or ammonium sulfate.
18. The composition of claim 12 , wherein the permeability enhancing agent comprises a polymer or a nanoparticle.
19. The composition of claim 12 , wherein the stabilizer is attached to the permeability enhancing agent.
20. The composition of claim 12 , wherein the stabilizer and the permeability enhancing agent are attached to a nanoparticle.
21. The composition of claim 14 , wherein the fixative comprises about 10-40% ethanol or about 10-40% methanol.
22. The composition of claim 14 wherein
the phosphatase inhibitor comprises sodium orthovanadate at a concentration of between about 100 mM and about 400 mM or beta glycerophosphate at a concentration of between about 375 mM and 1.5M,
the kinase inhibitor comprises staurosporine at a concentration of between about 5.0 uM and 20.0 uM or genistein at a concentration of between about 0.5 uM and 2.0 uM, and
the permeability enhancing agent comprises about 0.5% to about 15% polyethylene glycol.
23. A kit for fixing proteins in a sample, comprising the components of the composition of claim 12 and a sentinel comprising a particulate entity attached to one or more surrogate phosphoprotein markers, in one or more containers.
24. A composition for preserving a sample comprising proteins, said composition consisting essentially of:
a. a fixative that stabilizes the proteins in the sample and that has a sufficient water content for a stabilizer and/or a permeability enhancing agent to be soluble therein; and
b. a stabilizer, comprising (i) a kinase inhibitor and (ii) a phosphatase inhibitor;
c. a permeability enhancing agent; and
d. a cross-linking agent.
25. The composition of claim 24 further consisting essentially of a protease inhibitor.
26. A method for preserving proteins in a sample, comprising contacting the sample with the composition of claim 12 , under conditions effective for the preservation of proteins in the sample.
27. The method of claim 26 , further comprising analyzing the phosphorylation state of at least one phosphoprotein in the sample.
28. A method for preserving proteins in a sample, comprising contacting the sample with the composition of claim 24 , under conditions effective for the preservation of proteins in the sample.
29. The method of claim 28 , further comprising analyzing the phosphorylation state of at least one phosphoprotein in the sample.