Genes associated with dasatinib sensitivity
The invention relates to a method for the Cell Type specific labeling with Amino acid Precursors (CTAP). In particular, the disclosed method permits the incorporation of stable isotope-labeled amino acids into the proteome of a vertebrate cell that has been engineered to express an exogenous enzyme that enables the cell to produce an essential amino acid from its amino acid substrate. The method employs stable isotope-labeled amino acid substrate/precursors from which essential amino acids bearing the label are generated. The labeled amino acids generated by the transgenic cell not only supports growth but specifically labels proteins of the transgenic cell. Furthermore, the use of different populations of cells expressing different exogenous amino acid-producing enzymes permits differential labeling of the proteomes of the individual cell populations in multicellular environments.
1. A method of selecting treatment with dasatinib for a prostate cancer patient comprising:
(a) contacting RNA from a circulating tumor cell (CTC) obtained from the patient with a primer set for measuring expression of gene products of genes TACSTD2, SPAN8, COL3A 1, SPOCK1, SFN, KRT7, and S100A2, the set comprising a plurality of synthetic oligonucleotide primers, each of which is capable of hybridizing to an expression product of one of said genes such that the plurality of primers can detect the gene products of all of said genes to measure the relative expression of each of said genes in the CTC from the patient;
(b) contacting RNA from a known dasatinib-sensitive cell with a primer set for measuring expression of gene products of genes TACSTD2, TSPAN8, COL3A1, SPOCK1, SFN, KRT7, and S100A2, the set comprising a plurality of synthetic oligonucleotide primers, each of which is capable of hybridizing to an expression product of one of said genes such that the plurality of primers can detect the gene products of all of said genes to measure the relative expression of each of said genes in said known dasatinib-sensitive cell;
(c) comparing the expression level of said genes in the CTC from the patient with the expression level of said genes in a known dasatinib-sensitive cell;
(d) treating the patient with dasatinib when the expression level of the genes in the CTC is equal to or less than the expression level of the genes in a known dasatinib-sensitive cell.
2. A method of selecting dasatinib treatment for a prostate cancer patient, the method comprising:
(a) contacting RNA from a CTC obtained from the patient with a primer set for measuring expression of gene products of genes TACSTD2, TSPAN8, COL3A1, SPOCK1, SFN, KRT7 and S100A2, the set comprising a plurality of synthetic oligonucleotide primers, each of which is capable of hybridizing to an expression product of one of said genes such that the plurality of primers can detect the gene products of all of said genes to measure the relative expression of each of said genes in said CTC;
(b) assigning a score between 0 and 100 to said expression value using the formula
SCORE
CT
=
100000
×
[
(
0.00657
×
log
2
(
2
-
COL
3
A
1
CT
2
-
GAPDH
CT
)
)
-
(
0.127
×
log
2
(
2
-
KRT
7
CT
2
-
GAPDH
CT
)
)
-
(
0.00246
×
log
2
(
2
-
SFN
CT
2
-
GAPDH
CT
)
)
-
(
0.206
×
log
2
(
2
-
S
100
A
2
CT
2
-
GAPDH
CT
)
)
+
(
0.000893
×
log
2
(
2
-
SPOCK
1
CT
2
-
GAPDH
CT
)
)
-
(
0.0838
×
log
2
(
2
-
TACSTD
2
CT
2
-
GAPDH
CT
)
)
+
(
0.525
×
log
2
(
2
-
TSPAN
8
CT
2
-
GAPDH
CT
)
)
-
1835
]
÷
4938
wherein a score ≤60 indicates a dasatinib sensitive profile and a score >60 indicates a resistant profile;
(c) treating the patient with dasatinib when the score is <60.
3. A method for selecting dasatinib treatment for a prostate cancer patient comprising:
(a) contacting RNA from a CTC obtained from the patient with a primer set for measuring expression of gene products of genes TACSTD2, TSPAN8, COL3A1, SPOCK1, SFN, KRT7, and S100A2, the set consisting of a plurality of synthetic oligonucleotide primers, each of which is capable of hybridizing to an expression product of one of said genes such that the plurality of primers can detect the gene products of every one of said genes to measure the relative expression of each of said genes in the CTC;
(b) calculating a sensitivity score for each cell using one of formulas:
SCORE
Affy
=
(
0.114
*
TACSTD
2
Affy
)
-
(
0.703
*
TSPAN
8
Affy
)
-
(
0.036
*
COL
3
A
1
Affy
)
-
(
0.002
*
SPOCK
1
Affy
)
+
(
0.022
*
SFN
Affy
)
+
(
0.514
*
KRT
7
Affy
)
+
(
0.518
*
S
100
A
2
Affy
)
Eqn
.
1
SCORE
CT
=
1000
*
[
(
0.00657
×
log
2
(
2
-
COL
3
A
1
CT
2
-
GAPDH
CT
)
)
-
(
0.127
×
log
2
(
2
-
KRT
7
CT
2
-
GAPDH
CT
)
)
-
(
0.00246
×
log
2
(
2
-
SFN
CT
2
-
GAPDH
CT
)
)
-
(
0.206
×
log
2
(
2
-
S
100
A
2
CT
2
-
GAPDH
CT
)
)
+
(
0.000893
×
log
2
(
2
-
SPOCK
1
CT
2
-
GAPDH
CT
)
)
-
(
0.0838
×
log
2
(
2
-
TACSTD
2
CT
2
-
GAPDH
CT
)
)
+
(
0.525
×
log
2
(
2
-
TSPAN
8
CT
2
-
GAPDH
CT
)
)
]
Eqn
.
2
or
SCORE
CT
=
100000
×
[
(
0.00657
×
log
2
(
2
-
COL
3
A
1
CT
2
-
GAPDH
CT
)
)
-
(
0.127
×
log
2
(
2
-
KRT
7
CT
2
-
GAPDH
CT
)
)
-
(
0.00246
×
log
2
(
2
-
SFN
CT
2
-
GAPDH
CT
)
)
-
(
0.206
×
log
2
(
2
-
S
100
A
2
CT
2
-
GAPDH
CT
)
)
+
(
0.000893
×
log
2
(
2
-
SPOCK
1
CT
2
-
GAPDH
CT
)
)
-
(
0.0838
×
log
2
(
2
-
TACSTD
2
CT
2
-
GAPDH
CT
)
)
+
(
0.525
×
log
2
(
2
-
TSPAN
8
CT
2
-
GAPDH
CT
)
)
-
1835
]
÷
4938
;
Eqn
.
3
and
(c) comparing the sensitivity score for the CTC with the sensitivity score for a known dasatinib-sensitive cell;
(d) treating the patient with dasatinib when the sensitivity score for the CTC is equal to or less than the sensitivity score for the known dasatinib-sensitive cell.
4. The method of claim 2 , wherein said relative expression of gene products is determined using polymerase chase reaction (PCR).
5. The method of claim 4 , wherein the PCR platform is a microfluidic RT-PCR platform.
6. The method of claim 2 , wherein said circulating tumor cell is EpCAM + CD45 − DAPI − .
7. The method of claim 2 , where said circulating tumor cell is isolated using flow cytometry.
8. The method of claim 3 , wherein the sensitivity score is calculated using Eqn. 1 and microarray data as input.
9. The method of claim 3 , wherein the sensitivity score is calculated using Eqn. 2 or Eqn. 3 and RT-PCR expression data as input.
10. The method of claim 2 , wherein said gene product is RNA or cDNA.
11. The method of claim 3 , wherein said expression product is RNA or cDNA.