1. A method for diagnosing cancer or predicting cancer-therapy outcome in a subject, said method comprising the steps of:
a) obtaining a sample from the subject,
b) selecting a marker from a pathway related to cancer,
c) screening for a simultaneous aberrant expression level of two or more markers in the same cell from the sample, and
d) scoring their expression level as being aberrant when the expression level detected is above or below a certain detection threshold coefficient, wherein the detection threshold coefficient is determined by comparing the expression levels of the samples obtained from the subjects to values in a reference database of sample phenotypes obtained from subjects with either a known diagnosis or known clinical outcome after therapy, wherein the presence of an aberrant expression level of two or more markers in individual cells and presence of cells aberrantly expressing two or more such markers is indicative of a cancer diagnosis or a prognosis for cancer-therapy failure in the subject.
2. The method of claim 1, wherein said sample phenotype is selected from the group consisting of cancer, non-cancer, recurrence, non-recurrence, relapse, non-relapse, invasiveness, non-invasiveness, metastatic, non-metastatic, localized, tumor size, tumor grade, Gleason score, survival prognosis, lymph node status, tumor stage, degree of differentiation, age, hormone receptor status, PSA level, histologic type, and disease free survival.
3. The method of claim 1, wherein said threshold coefficient has an absolute value .gtoreq.0.5.
4. The method of claim 1, wherein said threshold coefficient has an absolute value .gtoreq.0.6.
5. The method of claim 1, wherein said threshold coefficient has an absolute value .gtoreq.0.7.
6. The method of claim 1, wherein said threshold coefficient has an absolute value .gtoreq.0.8.
7. The method of claim 1, wherein said threshold coefficient has an absolute value .gtoreq.0.9.
8. The method of claim 1, wherein said threshold coefficient has an absolute value .gtoreq.0.95.
9. The method of claim 1, wherein said threshold coefficient has an absolute value .gtoreq.0.99.
10. The method of claim 1, wherein said threshold coefficient has an absolute value .gtoreq.0.995.
11. The method of claim 1, wherein said threshold coefficient has an absolute value .gtoreq.0.999.
12. The method of claim 1, wherein the aberrant co-expression level of the markers is indicative of the presence of cancer in the subject.
13. The method of claim 1, wherein the aberrant co-expression level of the markers is predictive of cancer-therapy failure in the subject.
14. The method of claim 1, wherein the cancer pathways are selected from the group consisting of the Polycomb pathway, the Polycomb pathway target genes, the \u201cstemness\u201d pathways, and the DNA methylation pathways.
15. The method of claim 1, wherein the cancer pathway is selected from the group consisting of the BMI1, Ezh2, Suz12, Suz12PolII, EED, PcG-TF, BCD-TF, TEZ, NanogSox2Oct4, Myc, He2neu, CCND1, E2F3, PI3K, beta-catenin, ras, src, PTEN, p53, Rb, p16ARF, p21, Wnt, and Hh pathways.
16. The method of claim 1, wherein the markers are selected from the group consisting of BMI1, Ezh2, H2A, H3, transcription factors, and methylation patterns.
17. The method of claim 16, wherein the aberrant co-expression level detected is of BMI1 and Ezh2.
18. The method of claim 16, wherein aberrant co-expression level detected is of H2A and H3.
19. The method of claim 1, wherein the markers being detected are in the form of either mRNA, microRNA, DNA, or protein.
20. The method of claim 1, wherein the genes are selected from the group consisting of ADA, AMACR+p63, ANK3, BCL2L1, BIRC5, BMI-1, BUB1, CCNB1, CCND1, CES1, CHAF1A, CRIP1, CRYAB, ESM1, EZH2, FGFR2, FOS, Gbx2, HCFC1, IER3, ITPR1, JUNB, KLF6, K167, KNTC2, MGC5466, Phc1, RNF2, Suz12, TCF2, TRAP100, USP22, Wnt5A and ZFP36.
21. The method of claim 1, wherein the aberrant expression level of two or more markers is detected by subjecting the cells to an analysis selected from the group consisting of multicolor quantitative immunofluorescence co-localization analysis, fluorescence in situ hybridization, and quantitative RT-PCR analysis.
22. The method of claim 1, wherein the threshold level is determined by comparing to the values in the reference database of samples obtained from subjects with known diagnosis or known clinical outcome after therapies.
23. A method of determining a detection threshold coefficient for classifying a sample phenotype from a subject, the method comprising the steps of:
a) obtaining a sample from the subject,
b) selecting two or more markers from a pathway related to cancer,
c) screening for a simultaneous aberrant expression level of the two or more markers in the same cell from the sample;
d) scoring the marker expression in the cells by comparing the expression levels of the samples obtained from the subjects to values in a reference database of samples obtained from subjects with either a known diagnosis or known clinical outcome after therapy, and
e) determining the detection threshold coefficient for the sample classification accuracy at different detection thresholds using reference database of samples from subjects with known phenotypes.
24. The method of claim 23, further comprising determining the best performing magnitude of said detection threshold and using said magnitude to assess the reliability of said established detection threshold in classifying a sample phenotype.
25. The method of claim 24, further comprising using the best performing magnitude of said detection threshold to score an unclassified sample and assign a sample phenotype to said sample.
26. The method of claim 23, wherein the two or more markers are selected from the genes identified in FIGS. 27-38.
27. The method of claim 23, wherein the cancer pathways are selected from the group consisting of the Polycomb pathway, the Polycomb pathway target genes, the \u201cstemness\u201d pathways, and the DNA methylation pathways.
28. The method of claim 23, wherein the cancer pathway is selected from the group consisting of the BMI1, Ezh2, Suz12, Suz12PolII, EED, PcG-TF, BCD-TF, TEZ, NanogSox2Oct4, Myc, He2neu, CCND1, E2F3, PI3K, beta-catenin, ras, src, PTEN, p53, Rb, p16ARF, p21, Wnt, and Hh pathways.
29. The method of claim 23, wherein the markers being detected are in the form of either mRNA, microRNA, DNA, or protein.
30. The method of claim 23, wherein the genes are selected from the group consisting of ADA, AMACR+p63, ANK3, BCL2L1, BIRC5, BMI-1, BUB1, CCNB1, CCND1, CES1, CHAF1A, CRIP1, CRYAB, ESM1, EZH2, FGFR2, FOS, Gbx2, HCFC1, IER3, ITPR1, JUNB, KLF6, K167, KNTC2, MGC5466, Phc1, RNF2, Suz12, TCF2, TRAP100, USP22, Wnt5A and ZFP36.
31. A method for simultaneously detecting an aberrant co-expression level of two or more markers a single cell, said method comprising the steps of:
a) obtaining a sample of tissue,
b) selecting a marker defined by a pathway,
c) screening for a simultaneous aberrant expression level of the two or more markers, and
d) scoring their expression level as being aberrant when the expression level detected is above or below a certain detection threshold coefficient, wherein the detection threshold coefficient is determined by comparing the expression levels of the samples obtained from the subjects to values in a reference database of sample phenotypes obtained from subjects with either a known diagnosis or known clinical outcome after therapy.
32. The method of claim 31, wherein the cancer pathway is selected from the Polycomb or \u201cstemness\u201d pathway.
33. The method of claim 31, wherein the markers are selected from the group consisting of BMI1, Ezh2, H2A, H3, transcription factors, and methylation patterns.
34. The method of claim 33, wherein the aberrant co-expression level detected is of BMI1 and Ezh2.
35. The method of claim 34, wherein aberrant co-expression level detected is of H2A and H3.
36. The method of claim 31, wherein the markers being detected are in the form of either mRNA, microRNA, DNA, or protein.
37. The method of claim 31, wherein the markers are selected from the group consisting of ADA, AMACR+p63, ANK3, BCL2L1, BIRC5, BMI-1, BUB1, CCNB1, CCND1, CES1, CHAF1A, CRIP1, CRYAB, ESM1, EZH2, FGFR2, FOS, Gbx2, HCFC1, IER3, ITPR1, JUNB, KLF6, K167, KNTC2, MGC5466, RNF2, Suz12, TCF2, TRAP100, USP22, Wnt5A and ZFP36.
38. The method of claim 31, wherein the aberrant expression level of two or more markers is detected by subjecting the cells to an analysis selected from the group consisting of multicolor quantitative immunofluorescence co-localization analysis, fluorescence in situ hybridization, and quantitative RT-PCR analysis.
39. A kit comprising marker sample collection means and means for detecting the simultaneous aberrant expression level of two or more markers in the same cell from the sample.
40. The kit of claim 39, wherein the detection means are selected from the group consisting of protein-specific differentially-labeled fluorescent antibodies; protein-specific antibodies from different species; differentially labeled species-specific antibodies; DNA and RNA-based probes with different fluorescent dyes; and bar-coded nucleic acid- and protein-specific probes.
41. The kit of claim 39, wherein the expression of Ezh2 and BMI1 are measured.
42. The kit of claim 39, wherein the expression of H2A and H3 are measured.
43. The kit of claim 39, wherein transcription factors are measured.
44. The kit of claim 39, wherein methylation patterns are measures.
45. The kit of claim 39, wherein said probes have a unique combination of colors.
The claims below are in addition to those above.
All refrences to claim(s) which appear below refer to the numbering after this setence.
1. A compatibilizer comprising:
a thermoplastic elastomer; and
an acrylic polymer, wherein said thermoplastic elastomer and said acrylic polymer form an interpenetrating polymeric network.
2. The compatibilizer of claim 1, wherein said thermoplastic elastomer is selected from the group consisting of: Styrene-butadiene-styrene (SBS), Styrene-ethylene-butadient-styrene (SEBS), Ethylene propylene rubber (EPR), Ethylene propylene-diene rubber (EPDM), ethylene-octene(EO), ethylene-butadiene (EB), Thermoplastic polyurethane elastomer (TPU), Thermoplastic Olefin (TPO), Styrene-ethylene-propylene-styrene (SEPS), poli-hydroxy-butyrate (PHB), thermoplastic polyester elastomer (TPC-ET), or mixtures thereof.
3. The compatibilizer of claim 2, wherein said thermoplastic elastomer is SEPS (Styrene-ethylene-propylene-styrene).
4. The compatibilizer of claim 1, wherein said thermoplastic elastomer is in an amount of 10 to 30% ww.
5. The compatibilizer of claim 1, wherein said acrylic polymer is selected from the group consisting of: Polyvinyl alcohol (PVOH, PVA, or PVAI), Sodium polyacrylate, Ethylene maleic anhydride copolymer, Polyvinyl butyral (PVB), Polyvinyl formal (PVF), Polyvinyl nitrate (PVN), Polyvinyl acetate, Polyethylene oxide (PEO), Polyacrylate emulsion, poly(butyl acrylate), PVAc copolymer emulsion adhesive of vinyl acetate (VAM), polyacrylamide, poly(vinyl acetate), poly(methyl methacrylate), poly(butyl acrylate), poly methacrylamide, poly(N-methyl acrylamide), poly(N-ethyl acrylamide), poly(n-propyl acrylamide), poly(n-octyl acrylamide), poly(N,N-diethylacrylamide), poly(N,N-diethyl methacrylamide), polyacrylonitrile, poly(vinyl formate), poly(vinyl propionate), poly(methacrylic acid), poly(vinyl benzoic acid), poly isopropenyl benzoic acid), poly(crotonic acid), poly(sorbic acid), poly(glutonic acid), poly(\u03b2-styryl acrylic acid) or poly(acrylic acid) (PAA), or mixtures thereof.
6. The compatibilizer of claim 5, wherein said acrylic polymer is poly(acrylic acid).
7. The compatibilizer of claim 1, wherein said acrylic polymer is in an amount of 70 to 90% ww.
8. A method for preparing a compatibilizer, comprising the steps of:
a) heating water with a surfactant;
b) adding a thermoplastic elastomer;
c) adding an initiator; and
d) adding an acrylic monomer.
9. The method of claim 8, wherein said thermoplastic elastomer is selected from the group consisting of: Styrene-butadiene-styrene (SBS), Styrene-ethylene-butadiene-styrene (SEBS), Ethylene propylene rubber (EPR), Ethylene propylene-diene rubber (EPDM), ethylene-octene(EO), ethylene-butadiene (EB), Thermoplastic polyurethane elastomer (TPU), Thermoplastic Olefin (TPO), Styrene-ethylene-propylene-styrene (SEPS), poli-hydroxy-butyrate (PHB), thermoplastic polyester elastomer (TPC-ET), or mixtures thereof.
10. The method of claim 8, wherein said thermoplastic elastomer is in an amount of 10 to 30% ww.
11. The method of claim 8, wherein said acrylic monomer is selected from the group consisting of: vinyl alcohol, Sodium acrylate, vinyl butyral, vinyl formal, vinyl nitrate, vinyl acetate, ethylene oxide, acrylate emulsion, butyl acrylate, acrylamide, vinyl acetate, methyl methacrylate, butyl acrylate, methacrylamide, N-methyl acrylamide, N-ethyl acrylamide, n-propyl acrylamide, n-octyl acrylamide, N,N-diethylacrylamide, N,N-diethyl methacrylamide, acrylonitrile, vinyl formate, vinyl propionate, methacrylic acid, vinyl benzoic acid, isopropenyl benzoic acid, crotonic acid, sorbic acid, glutonic acid, \u03b2-styryl acrylic acid or acrylic acid, or mixtures thereof.
12. The method of claim 8, wherein said acrylic monomer is in an amount of 70 to 90% ww.
13. A method according to claim 8, wherein the compatibilizer is contacted with one or more recyclable plastic polymers.
14. A polymer mixture, comprising a compatibilizer as claimed in claim 1 and one or more recyclable plastic polymers.