Gene expression profiling of EGFR positive cancer
The present invention concerns prognostic markers associated with EGFR positive cancer. In particular, the invention concerns prognostic methods based on the molecular characterization of gene expression in paraffin-embedded, fixed tissue samples of EGFR-expressing cancer, which allow a physician to predict whether a patient is likely to respond well to treatment with an EGFR inhibitor.
1. A method for predicting the likelihood that a human colon cancer patient will exhibit a clinically beneficial patient response to treatment with cetuximab, the method comprising:
a) assaying a normalized level of a predictive RNA transcript in a sample comprising ErbB1-expressing colon cancer cells obtained from said patient, wherein the predictive RNA transcript is the transcript of laminin gamma 2 (LAMC2);
b) analyzing the normalized level of the LAMC2 transcript; and
c) predicting the likelihood of response of the patient to treatment with cetuximab by comparing the normalized level of the LAMC2 transcript to gene expression data obtained from reference samples derived from patients with colon cancer, wherein an increased normalized level of LAMC2 RNA transcript correlates with a decreased likelihood of response to treatment with cetuximab.
2. The method of claim 1 , wherein said sample is a tissue sample.
3. The method of claim 2 , wherein the tissue sample is fixed, paraffin-embedded, or fresh, or frozen.
4. The method of claim 2 , wherein the tissue sample is derived from fine needle, core, or other types of biopsy.
5. The method of claim 1 , further comprising the step of preparing a report comprising a statement whether the patient is likely to respond to treatment with cetuximab.
6. The method of claim 1 , wherein the normalized level of the LAMC2 RNA transcript is determined using an array comprising polynucleotides hybridizing to a LAMC2 gene immobilized on a solid surface.
7. The method of claim 6 , wherein said polynucleotides are cDNAs.
8. The method of claim 7 , wherein said cDNAs are about 500 to about 5000 bases.
9. The method of claim 6 , wherein said polynucleotides are oligonucleotides.
10. The method of claim 9 , wherein said oligonucleotides are about 20 to 80 bases long.
11. The method of claim 6 , wherein the array comprises about 330,000 oligonucleotides.
12. The method of claim 6 wherein said solid surface is glass.
13. The method of claim 2 , wherein RNA is isolated from colon cancer cells present in a fixed, paraffin-embedded tissue by a procedure comprising:
(a) incubating one or more sections of said fixed, paraffin-embedded tissue at a temperature of about 56° C. to 70° C. in a lysis buffer, in the presence of a protease, without prior dewaxing, to form a lysis solution;
(b) cooling the lysis solution to a temperature where the paraffin solidifies, thereby generating a cooled lysis solution; and
(c) isolating the RNA from said cooled lysis solution.
14. The method of claim 1 , further comprising the use of a kit comprising one or more of (1) extraction buffer/reagents for extracting mRNA from a sample and protocol; (2) reverse transcription buffer/reagents and protocol; and (3) quantitative polymerase chain reaction (qPCR) buffer/reagents and protocol suitable for performing the method of claim 1 .
15. The method of claim 6 , wherein said polynucleotides comprise modified and unmodified polynucleotides.