Molecular profiling of disease and therapeutic response using phospho-specific antibodies

A method for identifying protein biomarkers of patient responsiveness to a therapeutic composition having efficacy against a disease involving altered signal transduction, said method comprising the steps of:

• (a) obtaining tissue samples from a plurality of patients having said disease, said tissue samples comprising samples from patients (i) treated with said therapeutic composition, (ii) responsive to said therapeutic composition, and (iii) non-responsive to said therapeutic composition;
• (b) utilizing a panel of phospho-specific antibodies in a cellular assay to detect the phosphorylation statuses of a plurality of signal transduction proteins in said tissue samples;
• and
• (c) determining correlations between the phosphorylation statuses of said signal transduction proteins detected in step (b) and responsiveness to said therapeutic composition, wherein one or more significant correlation(s) identifies one or more signal transduction protein(s) as biomarker(s) of patient responsiveness to said therapeutic composition.

A method for identifying protein biomarkers useful in disease prognosis, said method comprising the steps of:

• (a) obtaining tissue samples from a plurality of patients having a disease involving altered signal transduction, said tissue samples comprising (i) samples from patients having negative and positive disease outcomes, and/or (ii) samples from patients having early-stage and advanced disease;
• (b) utilizing a panel of phospho-specific antibodies in a cellular assay to detect the phosphorylation statuses of a plurality of signal transduction proteins in said tissue samples;
• and
• (c) determining correlations between the phosphorylation statuses of said signal transduction proteins detected in step (b) and progression or outcome of said disease in said patients, wherein one or more significant correlation(s) identifies one or more signal transduction protein(s) as biomarker(s) useful in disease prognosis.

A method for selecting a breast cancer patient likely to respond to a therapeutic composition targeting Epidermal Growth Factor Receptor (EGFR) or HER2, said method comprising the steps of:

• (a) obtaining at least one tumor tissue sample from said patient;
• (b) determining, by cellular assay, the phosphorylation statuses of ERK, estrogen receptor (ER)(Ser118), mTOR and AKT in said tissue sample using phospho-specific antibodies;
• and
• (c) comparing the phosphorylation statuses detected in step (b) with a control sample to determine activation of ERK and AKT in said tissue sample relative to said control,
• wherein activation of both ERK and ER(Ser118), but not mTOR and AKT, in said tissue sample identifies said patient as having HER2-mediated cancer and thus likely to respond to a HER2-inhibitor, and
• wherein activation of ERK, ER(Ser118), mTOR, and AKT in said tissue sample identifies said patient as having EGFR-mediated cancer and thus likely to respond to an EGFR-inhibitor.